List of all items
Structs
- alphabet::DnaAlphabet
- alphabet::ProteinAlphabet
- alphabet::RnaAlphabet
- assembly::AssemblyStats
- bwt::Bwt
- codon::CodonUsage
- codon::GeneticCode
- debruijn::DeBruijnGraph
- debruijn::Unitig
- fasta::FastaStats
- fasta_index::FastaIndex
- fasta_index::FastaIndexEntry
- fasta_index::IndexedFastaReader
- fastq::FastqRecord
- fastq::FastqStats
- fm_index::FmIndex
- fmd_index::BiInterval
- fmd_index::FmdIndex
- kmer::KmerIter
- masking::DustParams
- masking::MaskResult
- masking::MaskedRegion
- masking::SegParams
- masking::TandemRepeatParams
- minhash::FracMinHash
- minhash::MinHash
- motif::DiscoveredMotif
- motif::MotifMatch
- motif::Pwm
- motif_io::Motif
- orf::OrfResult
- paired::PairedFastqRecord
- paired::PairedFastqStats
- protein_properties::AminoAcidComposition
- protein_properties::DisorderPrediction
- protein_properties::ExtinctionCoefficient
- protein_properties::SecondaryStructurePrediction
- pssm::Pssm
- quality::QualityScores
- read_sim::ReadSimConfig
- read_sim::SimulatedRead
- restriction::CutSite
- restriction::Fragment
- restriction::RestrictionEnzyme
- rna_structure::MfeResult
- rna_structure::NussinovResult
- rna_structure::PartitionResult
- rna_structure::RnaSecondaryStructure
- seq::ValidatedSeq
- suffix::SuffixArray
- taxonomy::KmerClassifier
- taxonomy::TaxonomyNode
- taxonomy::TaxonomyTree
- trim::PairedTrimReport
- trim::TrimPipeline
- trim::TrimRange
- trim::TrimReport
- twobit::TwoBitSequence
Enums
- codon::GeneticCodeId
- codon::SubstitutionClass
- masking::MaskMode
- masking::MaskSource
- motif::Strand
- motif_io::MotifAlphabet
- orf::Strand
- paired::MateValidation
- protein_properties::HydrophobicityScale
- protein_properties::SecondaryStructure
- quality::PhredEncoding
- restriction::Overhang
- taxonomy::TaxonRank
- trim::OrphanPolicy
- trim::PairedTrimResult
Traits
Functions
- assembly::assembly_stats
- assembly::nx_values
- codon::classify_substitution
- codon::codon_adaptation_index
- codon::count_syn_nonsyn_sites
- codon::translate_codon
- codon::translate_sequence
- fasta::parse_fasta_stats
- fastq::parse_fastq_file
- fastq::parse_fastq_stats
- masking::apply_mask
- masking::dust
- masking::find_tandem_repeats
- masking::mask_dust
- masking::mask_seg
- masking::seg
- motif::discover_motifs
- motif_io::motif_similarity
- motif_io::parse_jaspar
- motif_io::parse_meme
- motif_io::parse_transfac
- motif_io::write_jaspar
- motif_io::write_meme
- motif_io::write_transfac
- orf::find_orfs
- orf::find_orfs_both_strands
- orf::find_orfs_with_codons
- paired::deinterleave_fastq_file
- paired::interleave_fastq_files
- paired::parse_interleaved_fastq
- paired::parse_paired_fastq_files
- paired::parse_paired_fastq_stats
- paired::strip_read_suffix
- paired::validate_mate_pair
- paired::validate_mate_pair_strict
- paired::write_interleaved_fastq
- paired::write_paired_fastq
- pattern::bndm
- pattern::bom
- pattern::horspool
- pattern::kmp
- pattern::myers_bitparallel
- pattern::shift_and
- pattern::ukkonen
- protein_properties::amino_acid_composition
- protein_properties::chou_fasman
- protein_properties::extinction_coefficient
- protein_properties::gor
- protein_properties::gravy
- protein_properties::hydrophobicity_profile
- protein_properties::isoelectric_point
- protein_properties::predict_disorder
- pssm::dna_mapping
- pssm::protein_mapping
- read_sim::simulate_reads
- restriction::common_enzymes
- restriction::digest
- restriction::find_cut_sites
- restriction::fragment_sizes
- rna_structure::base_pair_distance
- rna_structure::mccaskill
- rna_structure::mountain_distance
- rna_structure::nussinov
- rna_structure::zuker_mfe
- trim::apply_trim
- trim::filter_by_length
- trim::filter_by_quality
- trim::filter_low_complexity
- trim::find_adapter_3prime
- trim::intersect_ranges
- trim::shannon_entropy
- trim::trim_adapter
- trim::trim_leading
- trim::trim_quality_3prime
- trim::trim_sliding_window
- trim::trim_trailing