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<meta name="author" content="Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology" />
<title>coverm contig usage</title>
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b1GPe7Jq5dxTuORZ11TZuHC3LD00fOhwI7OVWtVZygRPSeVUt0+D1Wq2mVGqiGX4zmNwOu8HOhccRljzgqoiArYV5DSXF1SDB1sddEk825YBijeRQiVcrvHAqyJ5Pv/3+k0l/7GwKzGzQ6Wa811i/qXFjfb0wlJ1jP/DXxwMGLpdcbNHcsTuWvv7ll29fOPPJXwAQpnMOLxWGxbIaK6VuPU3ySmaOmQ0cHDPPzVmNGM9qlJ1DHgNzu6hmOGTcZXYV9f8d8HTbUOn8QrbvuW11Tz3swiw0oRPvyPQu96Sywe9+2mlNGRBlVqGU88fB+dM97E+VvGCx2CV7ht/htgIgmqhez9mjt1FnRYR6bscerSYTkLTqvTcUDPLPA6osi+JOiG7ST//n2W+/++TCTLMsNCxmTzdu3Ny4evOmNS9gNlr5647tA/rh0V+/mfny+4Gv3r54+i+fxLF0cN44IRk6hdOTDF4jpdzqtkrxGit4uRskyaUyyqIw6paZQyiRZQ632++JsUuivNbh53Kb+x/2JYp/e/+7qFl8eecf/zBk65bfb7WQLstc2AZl1GMH9v3fJxx/p2pttp/+c/eGrS8oUksFoBYpHVxK3cVlMjkJ4UaSuj0GvhQMgKIsVkScspUqq0GtY98IAxWmOZS1p2QNgeJSXkPW3DX3mE+zrxreeANH3lObN6LH8KHopW83l9G3+3TugmsDC9PnPNkLgEKQuYQCzplcKIVu8HC4a56vQ5YpvYtY4ESnSHIzW6Vn+Qzd72xlLbYWV0R0nXpFDJm6XKvOqvPk5pJekVxrm/JekTY2T7teEU9KnHUa+zj/8pXd+rzbxD1uragaVBdAqDC+jaAUkrJv/OXKcGMXmJOnbhQXF/F3QsHJVnf87VhB3sSqoa/te5X9jf3r7FdPzMgtC/ccNOnTtwb3ZPb6ZWdOPLzh7amPD50/4z8/1T4uVE5ICkzt9ewxXYdBbfPqVx54ddvqMauTndXFnYfmBnY+2PS66ypEhs2ZFOn5IO08/ZFvfn4cEPYCCD24nnuUzM5i0nFz7dF7vEkWvcMhVEQcNgOA3q0Y7xjlCatesVT2mALbtRUfM1P06cfm/+GZhgadoWD/jBMnyJuLfn/kk+jrfHXnDOow4N5XP4gWAxDYDoDjxAtAwcr9tZ3PJCDa7Ga5MmImVlQ04/3EwqZSIqAJJVQc3NDQ1CG3TceObXI7CJWYU1Zc0qFDaSkAubaKudSxTZAEd4Q9TqPRrNP5kj22yognrLcC1z6ISzW5xSTOhATTljhb3v2det7Zv/eNGZnLt9g16B6h+aqNHZHv0yaP8TSV89QGJTzetxgMRqNOEkSdYHeYAGw2nY7KRje1xiKGfD5zeUyFyuJsRTUiQi0bdclYkzcER73JeuD5E2zOnB07dKSgy2icydpGlxLpQTZOcjW/XTo9NjcO5nNT4GQCoiASQHfca2tMVBjHYVRo6SRfJQGoCAfcdruDiz+gdwRo66xWHrfb4RPMPm5p0302p1UPDkUPuCLEt534Igi1bHVIVIgEzfAqepHh1bRDypryyOa1DVNmblnVsDhFl79rIuIAXcHhmYdfJicWLNj3cnSLcv/zx9HjQmV99dDDg8e8+heuMZq2cnxdUBBOApeiri69x23S22xcWW02g/V2ytpSV72Jmrp7m4JG6NDUt95RNPXwJ+q8d0XUSWM2dhSfU9EknsU6wSyDnOwzeLgds1GbYvxvmcVylSHFilGFxE4PYRT74fKaf/wOTZcvobX5lZ3PPffii88/10Cy2I/swyeR/AFNmMfeZ1f/8rfzH545p1j5vdyW1apU+6E8nOEzCrKsS3foHJkBwQhWq7siYrXprboUaHXDzMdZ0GLBqpaeO2hPAhMUr62Y+gRHrThpU8Niry7c+PBf/+f7yzvryabGFc8+6xowcMRg1kUqqh9azT5h/1GcNr14+GTWl29fevfUeYVXHNNSlVexqMKW6qHJyT6bL8OfnOK1pqalecxOp8wtv80MFRHz/+Y2VT5yJ1l63Ul6r3vQ0njtQyL9GzaIW15cvXnjnI8uf/fJ57P0SQsajObpM/d9mHXp3YunT59birloRDO2a6z/9T38eEzFCzE9okGOpw1ywy6zXm8wEF4DsZrB4FYtg03rc2nRkaE5IY15ZEfvjt4eRQtfaahz6rrsFoaZNlk/fTbaJFSenDQjlrnS6XyW1twOtIplrqLzeuZaEfHYJKq/rj/5t8pdueG5kbsG25Hfpq50+j/e/+tjA/bXzF82+dmN88r/evSPL3Z6ftEjj7Yds+J13jSzsaHnpjbt7h4Uvrdr2aAH+yzaXLm4R1W3O7p2KO71FCCkX/uG7BQrwKPWJlwu3jPioEKS1+C0OXtFLGGbVeaCkj1xU3kqIVjV5ONWqo52xVGXhtxKNuHyEMcdA5NSJuSy17ZurRiBXdlrw2vN8lyzHQeQZdU9/83mRWePngiAsIOvrjKhElx8fh86ZZPJ4DS4PSaz2aZzWdVV7TFqEbMS/4daVmW0rJcrhBY127EvX9TPNNQl6UP7Z7zztlAZLeMO6GMSvnpozV2Dj54hp7RcjgiVau+HAQ0ms6hHK6jhiJZl+NX0NFTicIYQt7ER+76ptuiMte/tYyP4oI/8o0cx9iPtrx6K5UpSgI/Winsblz4lNc3rsZipYBZ0yQ7ubnTuxCyYK7c2A1U2Z2Rlk8LhUHSq1BmbsoRPKeSfcBbp2qSdPsY+3jNxsk5nLHCcaHqjg0snBF7dzc6QBZ3OvHR/dK5QyUaz6j5l+4tJbXTp7trW9eRvHClACAIIOpXGzLBdFiVAUWlxQZ3RLaD1pnQ4ngmjmhUfYgteQT9m/JktwFVH2Cn27hFSQLxsGO6IfhU9jUdYD0AgfL1LfHw3z/sVMqnHK5jB7OBLO0UHfIJCVam1GRJo46KKOdrSUrLvuwFOnfnuS/tYTsWfl/StKu2xq3cXzuCVn9wf+pn87mrGy5vtC03HtkAsZ6YPCZW3yJl7RUQr6npF0P2/5cz0oeZ/ksHR0+TL6D5y31Q6eN685sPxrixetlPl5/YlJxu9AFbZRbmnpqlpTq09K3F7TdV/bpXcPJZTfEtxCddDvj7d3EK4ZLfHjedrpx794PFH58/49MClCxdM44aRZaRxE+aPjywnw0Zg4ebdS6Xj7NzZoCl4FhAvMxuZrfluorSo0RSABN+tlHzx8nKeJv3cDAiV7Ijaw5Oq4OwWDQ4H8UFqqsXiE2laujso0QScEzYFFXSDxYr7U7DPVNCV5Dj2pcRw4eKhDx+Z/9jjp45OnvHwVFIePIvB49LSPRvZ+yPvJcsjvOq5cRenZNg4zJn2qEvdpyXVQg6tAS/XAzu1JvkcpuoIdVglCaojEuTngS3pjfw38rSkOlOZT8nQVNOmbD9lKoU5HFg8t2TMUz2mRrqPyi95omTcisrHK/sMJSfuLFn/UKvsVinhsvqH/RkZSeoOPFuKdcJwrcuYCALV8343AGpSu4xtNPOWXcZcCQNO1/Xt0PNKk/Gszp3Ly0IVZPfVC2Lfxb3C5ZVhQDjK7fd5dVemazjNozNTahCARxo62irVJxKnwUz4SzDKgg+07k9ljt9sw2apra1KOJCldLR6NAOuqD89OWHNwpPHcdniPisKChY+tHv7My8sX/FdifTO+xlov4LNXXfvoH7vstCH5z462QkQypUYSDzBpV4Zzk5y6s3mZI+dGD1OMS3dlORL6h/R+3xOcNr6RpxJIPa5uRWkRdPQzZ6Nm29lf5Lfinl2ypuduEqQxqONXTatnD0HG9jQblU05erVU2+99f/EEzUL+/1uGTs397MxS+7YtDz/xwtzsfO+U4psZqMkeIVtnHNByAibW0GmBSxtctLd7iwZeNSYn1gJchaVBku9il8r9co82Ja9clCxDnKwNLs0IXQ6VLV4+OLx8+eOq7t/UVXVgmF14+YuGrN42MKqeVtnzHh627QZW8mHj01aNmxh794Lhz059ZEFD/CHvfj7JZN+N2XbM1Onbd8BiscDEJT9Fw8MDrdzWGSj0WYS9URPTS6LW/YmGSwW2So5HBScbqsz3UmsTqvThG7JlATlWg+33RHrzL7lpjuGUOGj1uaovjBEKnH2HjYCJfY6dmGv72BvYGd+ARu7j1wgZ5vZ3Ma57Ec08RslQBKsgaxUVYkkUR726QUqUDlmFjgmiYqtbgjFLYRiI5p/YebmnxVpXPuF1kupUABdeGdcdiE4pdy0Dj5fmkmCgNS13E07lbRqK/n1/mCviN+tt/WK6OGGznh/s4t9I39VVFmLztSUlwuwZdCiRC2l/Kk33lG0dHD/qprTbw5/ZmTxqMV9Z8yYvelw/cCqjf/+6K9P9H9t4KLl7R+cvmJR99W/f6Ggbs3LPQbRnMF1WW0mD5q1NDW4IJjSKdy5prTH+klDl+fctXrZxm5rs9r27dWuY8e8oqHTRvWb0MVZPfnuKWXOMUCwWLTQ8eKH6u5TWpiTanKAI8lnpW495N90QCAhzctKeI/FxVnZpaXZWcU4pzgrq7Q0K6tYnFrUrl1RYUFBYfwOQGEM7xzvEdt5hxKeSwWDXmrNT0936a1esbSDZAKH1ZRuIuCwOYjJYXKk5AWcoRQByhNPBdhblgFRMxHuG90bnN2obu8KDjc3eYHM1py5DiFU2NqhNXTQOXMWz10weE77sRWvffDZq0880vHB5vXv4PB3les1tv2D02z76xP2YNvdezD3pT3s7N497JOXhMCeTTu3t/2dq9X3n575qfMjIXZI/Q7b/u6brOGD0zj0rT+wD/+wB3P2xr8GQKCCushU8W1OdzqUhlt5pRQDokeJazP8rQwGh88D1EYJNTvSOakf3feGku9qVGpqG4xTV8ojfbXWGSt18iYUtdZJXEnDlt0/edPztWvHjM+btnB+HauecmLUlAeov2bk6HHjJkhCcGFoRIcJs1jnI2OaCgRBqd8NhFraSI+CBGbICTupxI21YNTrBbMkWKwmUYegHGS5WbPRiyhjVuw2EAfPVEriM1kjLsUhtexzTK9lO0kQ1/dk29mzvXB9yo23qh9EHfeDXhAhJWwiKKAki0J1RCSQr20nattixUJOXfM71Bv9Hhc+CdeuaV3LRAIbAAjXdUoX16r7wqGgF3iOLui5Zpn1JodXKu1gsnFoi9Pi0DmtjnQHAR63E4fT4bythikCCP22ZKVVoUS+hp0Bqm51Fnr+L2UjHz5YPXLwfRNx36B+l3eeXrwWxYbNVy/8n+pGrtwd7tNtSfXsNFaLo9jTdPZ89ub/pXB47YrkEiRpzW3r+oJ09UfBJLnmAoG5dBi5LJ5U83Z/2GIGp7L7nGwzHPNQhS3J7yWaAKe27LkytvA6c/fPn39g4Oqa+fun195VPX3qwLunC2vmH9i/oGZlTdOCgdOm3l0zdZoiv/GASic8yQYLAMhwBiA6Q93NqCLLub9OUmpcstOLaHGCwAsItnQvZqjyadHEUVx6cz+0JMt+sjy645vIQH91edGont0XbPj9msiaPXiIVI2/NHhk35IePbMLh0yeP6V6/ZPPA4KflKlzBqAsnGkVRaCONIPUOstxn/MhJ+nrRKMzxUmcTl2yP92s88eVhKvIfTe2KDHRmKtlyd/2PpPpA3vsPbRzw4w1sz/8snbmA6Or7+w+pUPP8mXDl2wVvqx+wJu//YmVHWb32L5q0oAeXXrkBYa2LZl5056LnkfvwhP6xD0X5YAIN3pyAOvaT85494494cnCD133dnN3O1oEqNZDegiV4IHicLJoMOhs4HS6dC6+LeC2ulLMRKks6LWkMWHX6XqfaELKyMnTOhsGs13PNCxJNkz+Z/0Qg6GhAeewK698pKaNLwyr2caOScrsU1mzMEJygRWCYYcgIoBopDa7TidSq4jaQa/8RJkG7MortqVTEvILI6Z9PL1rzacn//ov0pY1S3t/raYhx5WrKDBA2ED6Yh0dqvitsEECMJuofkCEQsyAJOqq2jzatUOseZR82L1nz+7xMwlZzIVNAOBQIge7xQhgUfrILXa7jtog/71CzQq3qDNoZYbSkOzBpo31obZtOw24a8BDQx4ubWIXRk7UT9S1Kckrtu+bHgSEvqQKP1d3kPleHwFKDSZuX2mGBGlK3sc5EGO7FpnEzw8MXLlQ8pQsvpNv4K4ld9471NP2/hFAoDt1kaPi26q3zgo7lONnEnBvHfMfbr3iP964r4XTTjgzJSYsWHJ0V/3qF3eu3/B8lN07fsKwYRMeGCZM3nHw8LPP7T+w/TH+b/YjjwCBau4hdsY9BF+ZRr1AgMrEoJdu5R/4fBhELEUxdqM72c5aTGef1+IQVnvjPTGxCb3wfhzek01IufGW24c+AOIZzq8gnCYLACAbHrsGKMNHNDV6EPR/osTBA8ziYuCw7Tjs+ThseQz2CwV2Ou3PYeV9xMZBVchkAMkvnuAQM34FFf4CxEZ9KD5qXmxUIBBiM2mNMBxSoY3Sba1zpQWwlbVVwCXk5EIqmmhqKj93lzEgkm2zG3tH7IEWecP9w+9rGZ4ohslCYnXDUm9MGF2J0ihbnJBfkf59Rs7q4vv9Y9X1ozq9+dbRTwPhSMnYbk2zOnXtXqqkXKHH1tZM7NOvw5ip2e0XjzjcWDEhMjB/yIz70jFvcU/eGRvmVKrdoPJ0bltbq9R1v/YaDgTdn4hNzIa84ltA1MLCGETS7SCOQSAGkdoSIv86xGsg3HKMrOsQE6CUQxiaKGmtgtyAkWIwIMNxKIN5QK4xAIk3MIIVnNA/fAdPM+wIOhPaRNEtuvROycm7kHm7iMHM7wabASUqOtByowkglmHm5an5G8bOiYau9y/SAF7vYVQ2zqR5UUeUXdxLDtMT0SMkNXqR9Lhag0cfURpetbZG/AvZr2jRHOZSOkc5ztkqzrMIAf55rM9N5VmbON8PqhxBs8aRmyFqoTwG4b4dxLFrV2MQyS0hsq5DTACHylWC/hhXgUA+gFip9id54Z5wod3t1glmAKcgCUk+rogS11erXC6/JJ+WL8jcIsuyoNfbqiJ6Kri17tNEXW55EDWhHZV7uVhLarxnM5QhVqpNqbM3bcJ9eBf+bn/07S9xNlt4lIyKtaWSunqyntWxHSQcba5nhhhNYrmqS+3jurSmJdWx7jiVLwUx3sKsmLb5bgdRi4YYhP92EMegKQaR3RIiX4PgeGy65RhZ1yEmwMdxnW4b5z7CQrQJJmEDGMEX1st6ino0mXXgy0+0x2rMHLeOu0ewbTh8BHua7RiLw9m2MThS2DCa/3fbaLyfPTsaR+CIsWwrAOXzv877434CJ6RAQFkZnnRvmsAPExtcAA6rqFMCF0+a32f2945YHTpRoDazQHnjnES1lrm3+Fq4+YgL/ygm0lglwc7fxSoM1BZEj3qKzovZ1zsLv1479tEH9ykddGe2jnx04rGmh6Mjpu/9zy/NwbFk68SdWpPhmOUDNr2FDyl9dMMXV699l61D26bmvgOVZjp2ZRN9qTc7xVdOrI9LlUxpXLoVMfk7Nb7fDFELp2MQKbeDOAZzYhAZLSGyrkNMgA3xlRNMtEfCbHWUTvF5CmKjOFSQeO/frHjvH9+pMOtFUbKDBB6vWeALiC8fs96sl2LdkZoVarkRrHVH8v9lCDcaJGexM+zzQ42NZ9GHnuYrO3mL5LvvUdvFy4zXWq/B6ei/V+5Y9yQAqv0oW6R0aK94ppxcMTUAXpMJUu25YkGhw5Hbrl12RaQd5LrV3S5tj+vm0xpaZCBL2vZIQjWCo6Q2/2lnOTKUqE/1UYJv5ZAOKb36Lxv32p+OTCrfUnn27ofnjujZq094yVz2TcPf/v7+58IPi6dX3OnPyC0L3b917LZdPTcF8w/0mVQxcHZN+cTisqHF1YMuXO0r7Nv3562c52pXkOTnPL8TACXovgLUVWlXOH6L57V56vN2t3t+7FP1eajFc/Gz689fe+UW3xc/vP58whegruiOKsCNGRZehzj+cwyiTQwCqAIhKbtXOVDENWdkOJQLre3tedlIaF+WlJTe3ghi5y4pbYNtKyK+AqGgV6RD66BdECyZQU+xzqKriLgsNtBaO9R97viBxZsNL1corarUot3Jy/+qHSkOv7bLFExMz5TiAMaaVIb/wg7NmPnUc0VVb4+a/3xO8a6Hj/0reqcOO967tWbwurHswpy73lz03Mt7Jg1ZtfPpwzvoK7OWGon8BOY/+yddrEUqp/ie+4eMYP/9+yRWGwjyVpav5k5sXH9/5MVNo2XdQ6Sw4ektO5V1zXc4lW4kzreeMU+JFaqnVDtxVIn1ikl8vyqRVppEbn5e21993vp2z4/9rD7PafGcS1R7PsEQk1d7TaLX/gqAo9URXolZHHYXKGOgqI3xIgApTICovZYRgzDHIa79iUMMSoA4xl6IQTg0iG84RDrHQ4OYwA4CqBbHZ9d89VRlx1zyq6euqsJ5fsnUqhXwYN5jsTttkj7YRp9eETFSj91nsfLIR0+9LqSttY3QmLJw6/3b430QyITiIlAqxdlBMcj/lHpUk+6gRVqnV4kwil39+e/sK5T/9sUYXdkp9n3vr4YN77ll3OW+pzc8v7NpC3vppe0vPUtC7Ev2FzR/cQmlWcInr25+cGHXgtrefZ6cNHMlm8b+taaRbXjh4Aku21jXgbraqmOrzaLyJC1RNqNUrt0Vk/1HquySb/e8drD6PPN2z4+p45Ngi+d8fu35a9/f4vtcJtrzCSkx3Wh3fS2Ph2YhR9gJVO1CD4WTPAaDTSACKjsZTifKZjMqJ/QQ8tX1yhOfG8nPjUN6iccXE96Pp8ejezqVFHXsFCrqot3J8iefZP/q3KW8Y1m4nPwYfwOUY3tEGCUsjvv7PvxEa3orl8vQ6iZn76u47uxt1M+b2Kjnf3P2ZWVxBdGcfXw7QXSpTl4Si1SnX6L2X2yaUjNt+Dw0Xd40o6Z25NzmV4rxTJ9pvAljfYjl95r63Iuxboyetf0XbEBQGjL6zuy7cMOvu8aRRcWffLRjTHRO6DzXjNjutSq5e2KSf0PVDI8mmZuf107VNOfWz4851OeBFs+5ZLXnE/yxtZarrfrYDqw6wr2xGWIjpKsAWu+I2t+VyXex0jOkFJfNZpfsrQMOsKeYPHqqT+NdjB7q5euvRZPnb3oYUWsXUUomXo/W9JUVbx7J4HugOKR748Sz333/yd8fMwk63mSElTs38OYRzF9LmyID2Efsvwpjn83sV86KdcDaFQ1NOXQi58u3ce/ZMxo1nF6Nmgn7Y/TmxejV+puEyuv9TaJArLfsb+Iw6gkU6UvxFLggHe4Ot0uSrE5nKpjtqZKY4bc6eDxpBaOR51hGGj+Vwg8UUAc4b5zk4det2ia1fWVJO2TlvZF9aafq7NnSl1EYN4y9zJ7BYRgeN5RaonxdR8+Rfs09fmXXEH+ecs89LqzDiTgeF3ljSZmwlZ1m55QTGn6hNi32qy1yujAU0iAXCmBQuG26zkI8nqx8t7tVlk4oDOW1Mbbh0RHvSCKixdiunWg32pIyxcyKCIieFj7YoVjVRAeseV9R9a0q5rdyvYktTFkxnyvWs/Nzup6pu8B+ROnrBae6djz2+InL0aAOq4Y/e8+QDVf9G154buPm5xvWCb3mrjKRjN+7vp4xEwtQh3q8Y+a0KbPYz19MYDO5tw1mkLIPz3985rOPP/10x9NP7wBEE68Q7pH8YFF6wGWwWXmN0KJs3CSfKkwsE/Igzx1QzhIE0DR3nLfB89CcmUMWLuFF2u+WPJGTu3C+t3TBoiIAgpP5iG2lhdp+kEMyxSpMejflw753u9KSrHUfcfpp29njxj46a8zY3z3YPRTq3rmsqJu4b9TM2lGjps8c3qFLlw78AkQdn+k78TN1N5wPn+Szg2gC/nKrZc73En4mKLYb3o4vKU6BwvQ0olRTQpJEXXkDB/TOLAxZRpmn39tucP/KjIL21tHmqcL5rLZZnbvMquO3Tl1n1aldEci5Ff/FEyCCePMvngykw+K/eMIh5f8VUtYgffQ49lB7+R0HUNTpQenhP6WBBkscHEs5y+QZ1WF29yx63DMUTVyicNM3RdTpRZly061Rq55Od5RisXIk/bGKDPGARzmLjqmfcouq/e4LkcAKAEQZizSpY1khOWwS0KwXbHbQUZP2M1+x3pUgbyrhA/vjeGG9tcNjs9M6maNnb2B4FnXTeR1Tw7TF6DZldL0ZRcHuMIs2WRn9LW10DWe/ei9JQJ4ELUkjOsxJ7m6+QYbnXvbTY2Ow6D6FHh/7lTTBZZSVLOtqB8g4iCCHzeZK+dC1Y38ymWJ3vb5SBnteXszG7cAfyXB6EYzgPBD/URrIP3Wr6u+OqQ9OmDF94qRp5JtZj/9u9sx5C/icym8TiHvgB8gGOwAEwU4c/M4nELJA1RaoJelK5ZPTbBAIlYikk0WuCInpvPM3e2CJ+16ASv2UpGqjUBAIkMRRWhRNSeqtK6QAyGYBkJXxUyYgEkE7ZYLxAQJIVjbPWkkXx4+ZIJRzr1gnnuT0TQ2Xp3rTPZ5kI5Hl5NZ2wZDslYJtjN4kb/+ILklMTUvtHyFp1rT0tPw0qqdJaUlpzsxM6BvJlJ0W3iDhg5ZN3bwwdMsfKruRW2ZQbuRlt9evdcorVpPyolGwuJT/dUDsCHUKOz4AWfRHQvA065Z1snHLxtW7/oddaNewgZANO4LY+n9OPN+rQSxmD80rC7ed1/Rm9/puaEacl3tH9TwUsfXIpYPVzprl6o4iBXdYT0AUtDAtYc3y+EuJtrjkUwGEVlI650ylKvE+5ABA/HNTwuf9lc+BgItUcf0/AgZwQedwuks0ypTyaYjSqY+iqLe60l3E5aIWOZ1mxPuV70toergeGwR4g0v8V2eKi0otVJZJ05xV7GHcsHQO+0ESk9LSjDup6913x/KzVKdeX9THFGzb1v5TDDfpQ45bECoJ9+43cBcf0nCXXr/F8/43notvxJ6rVEnqc1TWG05X9cp+AAQRKWiHl2Knck80KgqljCAC4Aq1QvJpPHP6XaxCImp1FiUv6pwAUXstt2Ud9NrbHGJCAsQx9ufEKktsFtJBzroOMYF9EK/V+GK1mv8PflNJUQAAAAABAAAAARmahXJJOF8PPPUACQgAAAAAAMk1MYsAAAAAyehMTPua/dUJoghiAAAACQACAAAAAAAAeAFjYGRg4Oj9u4KBgXPN71n/qjkXAUVQwU0Ap6sHhAB4AW2SA6wYQRRF786+2d3atm3b9ldQ27atsG6D2mFt2zaC2ra2d/YbSU7u6C3OG7mIowAgGQFlKIBldiXM1CVQQRZiurMEffRtDLVOYqbqhBBSS/ohgnt9rG+ooxYiTOXDMvUBGbnWixwgPUgnUoLMJCOj5n1IP3Oe1ImajzZpD0YOtxzG6rSALoOzOiUm6ps4K8NJPs6vc/4cZ1UBv4u85FoRnHWr4azjkRqYKFej8hP3eqCfDER61uyT44DbBzlkBTwZD8h8/sMabOD3ZmFWkAiUs5f4f2SFNZfv6iTPscW+jOHynEzEcLULuaQbivCdW5SDNcrx50uFYLzFHYotZl1umvNM1tgNWX+V/3gdebi3ThTgVEMWKYci4kHZhxBie3TYx3rHbGr+Pdo7x4dIHTKe5DFn+O/j+W2VnE3ooW6isf0LIUENvZs1gf/LHojJwdpplCP5gn/5gi26FoYa19ZVFOJ6Sxuoz/q2Ti20IKVJdnqvYJwnhfPH/2f6YHoQF30aZaK9J8T026RxH5fA/WPW/8IW4zkpnIfoFLifGB86v0ffm5nbyRs5iaHR3hNBD0HSfTzoPugRM+hdN0x052KoHLBS0tdgpidAiEesDsgWYO73RWQz2LWIwjqnMe/uYISQtlbyf2NlT9Q9PoBcBnrO6I5ELoMeyHkNnIXGdv809H/DXNOTeAEc0jWMJFcQxvFnto/5LjEvHrdbmh2Kji9aPL4839TcKPNAa6mlZUyOmZk6lzbPJ3bo56//Cz+Vaqqrat5rY8x7xnzxl3nvo+27jFnz8c/mI9Nmh2XBdMsilrBitsnD9rI8aiN5DI/jSftC9mIf9pMfIB4kHiI+hWfQY5aPAYYYYYwpcyfpMMX0aZzBWZzDeVygchGXcBlX8ApexWt4HW/gLbzNbnfwLt7DJ/p0TX4+Uucji1hCnY/U+cijVB7D46jzkb3Yh/3kB4gHiYeIT+EZ9JjlY4AhRhhjytxJOkwxfRpncBbncB4XqFzEJVzGFbyCV/EaXscbeAtvs9sdvIv3cjmftWavuWs2mg6byt3ooIsFOyx77Kos2kiWsIK/UVPDOjawiQmO4CgdxnAcJzClz2PVbNKsy2ZzvoncjQ66qE2kNpHaRJawgr9RU8M6NrCJCY6gNpFjOI4TmNIn36TNfGSH5RrssKtyN+59b410iF0sUFO0l2UJtY/8jU9rWMcGNjHBEUypf0z8mm7vZLvZaC/LzdhmV2XBvpBF25IlLJOvEFfRI+NjgCFGGGNK5Rs6Z7Ij/45yNzro4m9Ywzo2sIkJjuBj2ZnvLDdjGxntLLWzLGGZfIW4ih4ZHwMMMcIYUyq1s8xkl97bH0y3JkZyM36j/+58rvTQxwBDjDDGNzyVyX35Ccjd6KCLv2EN69jAJiY4go/lfr05F+Ua7CCzGx10sYA9tiWLxCWs2BfyN+Ia1rGBTUxwBEfpMIbjOIEpfdjHvGaTd9LJb0duRp2S1O1I3Y4sYZl8hbiKHhkfAwwxwhhTKt/QOZPfmY3//Ss3Y5tNpTpL9ZQeGR8DDDHCGN/wbCbdfHO5GbW51OZSm8sSlslXiKvokfExwBAjjDGlUpvLTBY0K5KbiDcT672SbXZY6k7lbnTQxQI1h+1FeZTKY3gcT2KvTWUf9pMZIB4kHiI+xcQzxGfpfA7P4wW8yG4eT/kYYIgRxvgb9TWsYwObmOAITlI/xf7TOIOzOIfzuEDlIi7hMq7gFbyK1/A63sBbeJtvdwfv4j28zyaP8QmVL/imL/ENJ5PJHt3RqtyMbbYlPfQxwBAjjPEN9ZksqkMqN6PuV7bZy7LDtuRudNDFwzx1FI/hcTzJp73Yh/3kB4gHiYeIT+EZ9JjlY4AhRhjjb1TWsI4NbGKCIzjJlCmcxhmcxTmcxwVcxCVcxhW8glfxGl7HG3gLbzPxDt7Fe/gY/+egvq0YCAEoCNa1n+KVyTUl3Q0uIhoe+3DnRfV7nXGOc5zjHOc4xznOcY5znOMc5zjHOc5xjnOc4xznOMc5znGOc5zjHOc4xznOcY5znOMc5zjHOc5xjnOc4xznOMc5znGOc5zjHOc4xznOcY5znOM8XZouTZemS1OAKcAUYAowBZgCTAHm3x31O7p3vNf5c1iXeBkEAQDFcbsJX0IqFBwK7tyEgkPC3R0K7hrXzsIhePPK/7c77jPM1yxSPua0WmuDzNcuNmuLtmq7sbyfsUu7De/xu9fvvvDNfN3ioN9j5pq0ximd1hmd1TmlX7iky7qiq7qmG3pgXYd6pMd6oqd6pud6oZd6pdd6p/f6oI/6pC/KSxvf9F0/1LFl1naRcwwzrAu7AHNarbW6oEu6rCu6qmu6ob9Y7xu+kbfHH1ZopCk25RVrhXKn4LCO6KiOGfvpd+R3is15xXmVWKGRptgaysQKpUwc1hEdVcpEysTI7xTbKHMcKzTSFDtCmVihkab4z0FdI0QQBAEUbRz6XLh3Lc7VcI/WN54IuxXFS97oH58+MBoclE1usbHHW77wlW985wcHHHLEMSecsUuPXMNRqfzib3pcllj5xd+0lSVW5nNIL3nF6389h+Y5NG3Thja0oQ1taEMb2tCGNrQn+QwjrcwxM93gJre4Y89mvsdb3vGeD3zkE5/5wle+8Z0fHHDIEceccMaOX67wNz3747gObCQAQhCKdjlRzBVD5be7rwAmfOMQsUvPLj279OzSYBks49Ibl97In/HCuNDGO+NOW6qlWqqlWqqlWqqlWqqYUkwpphTzifnEfII92IM92IM92IM92IM92IM92I/D4/A4PA6Pw+PwODwOj8M/f7kaaDXQyt7K3mqglcCVwNVAq4FWA60GWglZCVkJWQlZCVkJWQlZDbQyqhpoNdAPh3NAwCAAwwDM+7b2sg8kCjIO4zAO4zAO4zAO4zAO4zAO4zAO4zAO4zAO4zAO4zAO47AO67AO67AO67AO67AO67AO67AO67AO67AO67AO67AO63AO53AO53AO53AO53AO53AO53AO53AO53AO53AO53AO5xCHOMQhDnGIQxziEIc4xCEOcYhDHOIQhzjEIQ5xiEMd6lCHOtShDnWoQx3qUIc61KEOdahDHepQhzrUoQ6/h+P6RpIjiKEoyOPvCARUoK9LctP5ZqXTop7q/6H/0H+4P9yfPz82bdm2Y9ee/T355bS3/divDW9reFtDb4beDL0ZejP0ZujN0JuhN0Nvht4MvRl6M/Rm6M3w1of3PVnJSlaykpWsZCUrWclKVrKSlaxkJStZySpWsYpVrGIVq1jFKlaxilWsYhWrWMUqVrGa1axmNatZzWpWs5rVrGY1q1nNalazmtWsYQ1rWMMa1rCGNaxhDWtYwxrWsIY1rGENa1nLWtaylrWsZS1rWcta1rKWtaxlLWtZyzrWsY51rGMd61jHOtaxjnWsYx3rWMc61rEeTf1o6kdTP/84rpMqCKAYhmH8Cfy2JjuLCPiYPDH1Y+rH1I+pH1M/pn5M/Zh6FEZhFEZhFEZhFEZhFEZhFFZhFVZhFVZhFVZhFVZhFVbhFE7hFE7hFE7hFE7hFE7hFCKgCChPHQFlc7I52ZxsTgQUAUVAEVAEFAFFQBFQBBQBRUARUAQUAUVAEVAEFAFFQBFQti5bl63L1mXrsnXZuggoAoqAIqAIKAKKgCKgCCgCioAioAgoAoqAIqAIKAKKgCKgCCgCyt5GQBFQBPTlwD7OEIaBKAxSOrmJVZa2TsJcwJ6r0/+9sBOGnTDshOF+DndyXG7k7vfh9+n35fft978Thp2wKuqqqKtarmq58cY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<span class="author_name">coverm contig usage</span>
<span class="author_bio mbm">Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology</span>
<span class="author_bio mbm">2024-01-18 (coverm 0.7.0)</span>
</div>
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<div id="TOC" class="toc">
<ul>
<li><a href="#name">NAME</a></li>
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#read-mapping-parameters">READ MAPPING PARAMETERS</a></li>
<li><a href="#reference">REFERENCE</a></li>
<li><a href="#sharding">SHARDING</a></li>
<li><a href="#mapping-algorithm-options">MAPPING ALGORITHM OPTIONS</a></li>
<li><a href="#alignment-thresholding">ALIGNMENT THRESHOLDING</a></li>
<li><a href="#coverage-calculation-options">COVERAGE CALCULATION OPTIONS</a></li>
<li><a href="#output">OUTPUT</a></li>
<li><a href="#general-options">GENERAL OPTIONS</a></li>
<li><a href="#frequently-asked-questions-faq">FREQUENTLY ASKED QUESTIONS (FAQ)</a></li>
<li><a href="#exit-status">EXIT STATUS</a></li>
<li><a href="#examples">EXAMPLES</a></li>
<li><a href="#author">AUTHOR</a></li>
</ul>
</div>
<div id="post">
<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm contig - Calculate read coverage per-contig (version 0.7.0)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
<p><strong>coverm contig</strong> <MAPPING_INPUT> ..</p>
</div>
<div id="description" class="section level1">
<h1>DESCRIPTION</h1>
<p>coverm contig calculates the coverage of a set of reads on a set of contigs.</p>
<p>This process can be undertaken in several ways, for instance by specifying BAM files or raw reads as input, using different mapping programs, thresholding read alignments, using different methods of calculating coverage and printing the calculated coverage in various formats.</p>
<p>The source code for CoverM is available at <a href="https://github.com/wwood/CoverM" class="uri">https://github.com/wwood/CoverM</a></p>
</div>
<div id="read-mapping-parameters" class="section level1">
<h1>READ MAPPING PARAMETERS</h1>
<dl>
<dt><strong>-1</strong> <em>PATH ..</em></dt>
<dd><p>Forward FASTA/Q file(s) for mapping. These may be gzipped or not.</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>-2</strong> <em>PATH ..</em></dt>
<dd><p>Reverse FASTA/Q file(s) for mapping. These may be gzipped or not.</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>-c</strong>, <strong>--coupled</strong> <em>PATH ..</em></dt>
<dd><p>One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order <sample1_R1.fq.gz> <sample1_R2.fq.gz> <sample2_R1.fq.gz> <sample2_R2.fq.gz> ..</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--interleaved</strong> <em>PATH ..</em></dt>
<dd><p>Interleaved FASTA/Q files(s) for mapping. These may be gzipped or not.</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--single</strong> <em>PATH ..</em></dt>
<dd><p>Unpaired FASTA/Q files(s) for mapping. These may be gzipped or not.</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>-b</strong>, <strong>--bam-files</strong> <em>PATH</em></dt>
<dd><p>Path to BAM file(s). These must be reference sorted (e.g. with samtools sort) unless <code>--sharded</code> is specified, in which case they must be read name sorted (e.g. with <code>samtools sort -n</code>). When specified, no read mapping algorithm is undertaken.</p>
</dd>
</dl>
</div>
<div id="reference" class="section level1">
<h1>REFERENCE</h1>
<dl>
<dt><strong>-r</strong>, <strong>--reference</strong> <em>PATH</em></dt>
<dd><p>FASTA file of contigs e.g. concatenated genomes or metagenome assembly, or minimap2 index (with <code>--minimap2-reference-is-index</code>), strobealign index (with <code>--strobealign-use-index</code>), or BWA index stem (with <code>-p bwa-mem/bwa-mem2</code>). If multiple references FASTA files are provided and <code>--sharded</code> is specified, then reads will be mapped to references separately as sharded BAMs. [required unless <code>-b/--bam-files</code> is specified]</p>
</dd>
</dl>
</div>
<div id="sharding" class="section level1">
<h1>SHARDING</h1>
<dl>
<dt><strong>--sharded</strong></dt>
<dd><p>If <code>-b/--bam-files</code> was used: Input BAM files are read-sorted alignments of a set of reads mapped to multiple reference contig sets. Choose the best hit for each read pair. Otherwise if mapping was carried out: Map reads to each reference, choosing the best hit for each pair. [default: not set]</p>
</dd>
</dl>
</div>
<div id="mapping-algorithm-options" class="section level1">
<h1>MAPPING ALGORITHM OPTIONS</h1>
<p><strong>-p</strong>, <strong>--mapper</strong> <em>NAME</em></p>
<table>
<caption>Underlying mapping software used [default: <code>minimap2-sr</code>]. One of:</caption>
<thead>
<tr class="header">
<th align="left">name</th>
<th align="left">description</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left"><code>minimap2-sr</code></td>
<td align="left">minimap2 with '<code>-x sr</code>' option</td>
</tr>
<tr class="even">
<td align="left"><code>bwa-mem</code></td>
<td align="left">bwa mem using default parameters</td>
</tr>
<tr class="odd">
<td align="left"><code>bwa-mem2</code></td>
<td align="left">bwa-mem2 using default parameters</td>
</tr>
<tr class="even">
<td align="left"><code>minimap2-ont</code></td>
<td align="left">minimap2 with '<code>-x map-ont</code>' option</td>
</tr>
<tr class="odd">
<td align="left"><code>minimap2-pb</code></td>
<td align="left">minimap2 with '<code>-x map-pb</code>' option</td>
</tr>
<tr class="even">
<td align="left"><code>minimap2-hifi</code></td>
<td align="left">minimap2 with '<code>-x map-hifi</code>' option</td>
</tr>
<tr class="odd">
<td align="left"><code>minimap2-no-preset</code></td>
<td align="left">minimap2 with no '<code>-x</code>' option</td>
</tr>
</tbody>
</table>
<dl>
<dt><strong>--minimap2-params</strong> <em>PARAMS</em></dt>
<dd><p>Extra parameters to provide to minimap2, both indexing command (if used) and for mapping. Note that usage of this parameter has security implications if untrusted input is specified. '<code>-a</code>' is always specified to minimap2. [default: none]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--minimap2-reference-is-index</strong></dt>
<dd><p>Treat reference as a minimap2 database, not as a FASTA file. [default: not set]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--bwa-params</strong> <em>PARAMS</em></dt>
<dd><p>Extra parameters to provide to BWA or BWA-MEM2. Note that usage of this parameter has security implications if untrusted input is specified. [default: none]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--strobealign-params</strong> <em>PARAMS</em></dt>
<dd><p>Extra parameters to provide to strobealign. Note that usage of this parameter has security implications if untrusted input is specified. [default: none]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--strobealign-use-index</strong></dt>
<dd><p>Use a pregenerated index (one that has been created with 'strobealign --create-index'). The --reference option should be specified as the original FASTA file i.e. 'ref.fna' not 'ref.fna.r100.sti' [default: not set]</p>
</dd>
</dl>
</div>
<div id="alignment-thresholding" class="section level1">
<h1>ALIGNMENT THRESHOLDING</h1>
<dl>
<dt><strong>--min-read-aligned-length</strong> <em>INT</em></dt>
<dd><p>Exclude reads with smaller numbers of aligned bases. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-read-percent-identity</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by overall percent identity e.g. 95 for 95%. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-read-aligned-percent</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by percent aligned bases e.g. 95 means 95% of the read's bases must be aligned. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-read-aligned-length-pair</strong> <em>INT</em></dt>
<dd><p>Exclude pairs with smaller numbers of aligned bases. Implies --proper-pairs-only. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-read-percent-identity-pair</strong> <em>FLOAT</em></dt>
<dd><p>Exclude pairs by overall percent identity e.g. 95 for 95%. Implies --proper-pairs-only. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-read-aligned-percent-pair</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by percent aligned bases e.g. 95 means 95% of the read's bases must be aligned. Implies --proper-pairs-only. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--proper-pairs-only</strong></dt>
<dd><p>Require reads to be mapped as proper pairs. [default: not set]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--exclude-supplementary</strong></dt>
<dd><p>Exclude supplementary alignments. [default: not set]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--include-secondary</strong></dt>
<dd><p>Include secondary alignments. [default: not set]</p>
</dd>
</dl>
</div>
<div id="coverage-calculation-options" class="section level1">
<h1>COVERAGE CALCULATION OPTIONS</h1>
<p><strong>-m</strong>, <strong>--methods</strong> <em>METHOD</em></p>
<table>
<caption>Method(s) for calculating coverage [default: <code>mean</code>]. A more thorough description of the different methods is available at <a href="https://github.com/wwood/CoverM\#calculation-methods" class="uri">https://github.com/wwood/CoverM\#calculation-methods</a> but briefly:</caption>
<thead>
<tr class="header">
<th align="left">method</th>
<th align="left">description</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left"><code>mean</code></td>
<td align="left">(default) Average number of aligned reads overlapping each position on the contig</td>
</tr>
<tr class="even">
<td align="left"><code>trimmed_mean</code></td>
<td align="left">Average number of aligned reads overlapping each position after removing the most deeply and shallow-ly covered positions. See <code>--trim-min</code>/<code>--trim-max</code> to adjust.</td>
</tr>
<tr class="odd">
<td align="left"><code>coverage_histogram</code></td>
<td align="left">Histogram of coverage depths</td>
</tr>
<tr class="even">
<td align="left"><code>covered_bases</code></td>
<td align="left">Number of bases covered by 1 or more reads</td>
</tr>
<tr class="odd">
<td align="left"><code>variance</code></td>
<td align="left">Variance of coverage depths</td>
</tr>
<tr class="even">
<td align="left"><code>length</code></td>
<td align="left">Length of each contig in base pairs</td>
</tr>
<tr class="odd">
<td align="left"><code>count</code></td>
<td align="left">Number of reads aligned to each contig. Note that supplementary alignments are not counted.</td>
</tr>
<tr class="even">
<td align="left"><code>metabat</code></td>
<td align="left">("MetaBAT adjusted coverage") Coverage as defined in Kang et al 2015 <a href="https://doi.org/10.7717/peerj.1165" class="uri">https://doi.org/10.7717/peerj.1165</a></td>
</tr>
<tr class="odd">
<td align="left"><code>reads_per_base</code></td>
<td align="left">Number of reads aligned divided by the length of the contig</td>
</tr>
<tr class="even">
<td align="left"><code>rpkm</code></td>
<td align="left">Reads mapped per kilobase of contig, per million mapped reads</td>
</tr>
<tr class="odd">
<td align="left"><code>tpm</code></td>
<td align="left">Transcripts Per Million as described in Li et al 2010 <a href="https://doi.org/10.1093/bioinformatics/btp692" class="uri">https://doi.org/10.1093/bioinformatics/btp692</a></td>
</tr>
</tbody>
</table>
<dl>
<dt><strong>--min-covered-fraction</strong> <em>FRACTION</em></dt>
<dd><p>Contigs with less covered bases than this are reported as having zero coverage. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--contig-end-exclusion</strong> <em>INT</em></dt>
<dd><p>Exclude bases at the ends of reference sequences from calculation [default: <code>75</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--trim-min</strong> <em>FRACTION</em></dt>
<dd><p>Remove this smallest fraction of positions when calculating trimmed_mean [default: <code>5</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--trim-max</strong> <em>FRACTION</em></dt>
<dd><p>Maximum fraction for trimmed_mean calculations [default: <code>95</code>]</p>
</dd>
</dl>
</div>
<div id="output" class="section level1">
<h1>OUTPUT</h1>
<dl>
<dt><strong>-o</strong>, <strong>--output-file</strong> <em>FILE</em></dt>
<dd><p>Output coverage values to this file, or '-' for STDOUT. [default: output to STDOUT]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--output-format</strong> <em>FORMAT</em></dt>
<dd><p>Shape of output: 'sparse' for long format, 'dense' for species-by-site. [default: dense]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--no-zeros</strong></dt>
<dd><p>Omit printing of genomes that have zero coverage. [default: not set]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--bam-file-cache-directory</strong> <em>DIRECTORY</em></dt>
<dd><p>Output BAM files generated during alignment to this directory. The directory may or may not exist. Note that BAM files in this directory contain all mappings, including those that later are excluded by alignment thresholding (e.g. --min-read-percent-identity) or genome-wise thresholding (e.g. --min-covered-fraction). [default: not used]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--discard-unmapped</strong></dt>
<dd><p>Exclude unmapped reads from cached BAM files. [default: not set]</p>
</dd>
</dl>
</div>
<div id="general-options" class="section level1">
<h1>GENERAL OPTIONS</h1>
<dl>
<dt><strong>-t</strong>, <strong>--threads</strong> <em>INT</em></dt>
<dd><p>Number of threads for mapping, sorting and reading. [default: 1]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>-h</strong>, <strong>--help</strong></dt>
<dd><p>Output a short usage message. [default: not set]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--full-help</strong></dt>
<dd><p>Output a full help message and display in 'man'. [default: not set]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--full-help-roff</strong></dt>
<dd><p>Output a full help message in raw ROFF format for conversion to other formats. [default: not set]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>-v</strong>, <strong>--verbose</strong></dt>
<dd><p>Print extra debugging information. [default: not set]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>-q</strong>, <strong>--quiet</strong></dt>
<dd><p>Unless there is an error, do not print log messages. [default: not set]</p>
</dd>
</dl>
</div>
<div id="frequently-asked-questions-faq" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS (FAQ)</h1>
<p><strong>Can the temporary directory used be changed?</strong> CoverM makes use of the system temporary directory (often <code>/tmp</code>) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the <code>TMPDIR</code> environment variable e.g. to set it to use the current directory: <code>TMPDIR=. coverm genome <etc></code></p>
<p><strong>For thresholding arguments e.g. \-\-dereplication\-ani and \-\-min\-read\-percent\-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified?</strong> Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.</p>
</div>
<div id="exit-status" class="section level1">
<h1>EXIT STATUS</h1>
<dl>
<dt><strong>0</strong></dt>
<dd><p>Successful program execution.</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>1</strong></dt>
<dd><p>Unsuccessful program execution.</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>101</strong></dt>
<dd><p>The program panicked.</p>
</dd>
</dl>
</div>
<div id="examples" class="section level1">
<h1>EXAMPLES</h1>
<dl>
<dt>Calculate mean coverage from reads and assembly</dt>
<dd><p><strong>$ coverm contig --coupled read1.fastq.gz read2.fastq.gz --reference assembly.fna</strong></p>
</dd>
<dt>Calculate MetaBAT adjusted coverage from a sorted BAM file, saving the unfiltered BAM files in the saved_bam_files folder</dt>
<dd><p><strong>$ coverm contig --method metabat --bam-files my.bam --bam-file-cache-directory saved_bam_files</strong></p>
</dd>
</dl>
</div>
<div id="author" class="section level1">
<h1>AUTHOR</h1>
<blockquote>
<pre><code>Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology <benjwoodcroft near gmail.com></code></pre>
</blockquote>
</div>
</article>
</div>
</div>
</div>
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