nanalogue

Nanalogue = Nucleic Acid Analogue

Nanalogue is a tool to parse or analyse BAM/Mod BAM files with a single-molecule focus.

Commands

All the commands below have options you can specify on the command line. Please run --help with a command to learn what the options are.

nanalogue read-table-hide-mods

Prints basecalled length, alignment length, read id, and optionally other information such as sequence per molecule. This command does not expect modification data at all.

nanalogue read-table-show-mods

Prints basecalled length, alignment length, read id, modification counts, and optionally other information such as sequence per molecule. If modification data is not available, any modification-related columns have outputs like "NA".

nanalogue read-stats

Calculates various summary statistics on all reads

nanalogue read-info

Prints information about reads

nanalogue find-modified-reads

Find names of modified reads through criteria specified by sub commands

nanalogue window-dens

Output windowed densities of reads

nanalogue window-grad

Output windowed gradients of reads

Acknowledgments

This software was developed at the Earlham Institute in the UK. This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, through the Core Capability Grant BB/CCG2220/1 at the Earlham Institute and the Earlham Institute Strategic Programme Grant Cellular Genomics BBX011070/1 and its constituent work packages BBS/E/ER/230001B (CellGen WP2 Consequences of somatic genome variation on traits). The work was also supported by the following response-mode project grants: BB/W006014/1 (Single molecule detection of DNA replication errors) and BB/Y00549X/1 (Single molecule analysis of Human DNA replication). This research was supported in part by NBI Research Computing through use of the High-Performance Computing system and Isilon storage.