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bioconda-recipes

Conda recipes for the bioconda channel.

bitvector

C++ thread safe bitvector implementation

bowtie2

A fast and sensitive gapped read aligner

camisim

CAMISIM: Simulating metagenomes and microbial communities

compute-cormat

Compute large correlation matrix with BLAS routines

count-genes-connections

count-matrix-conv

count_matrix_to_sqlite_db

countmatrixdownsizer

Rarefies OTUs or genes raw abundance profiles to even sequencing depth across samples.

countmatrixtransformer

Compute relative gene abundance from raw read counts

cppstats

csfasta-fasta-conv

Program that converts files from csfasta format to fasta and the other way around.

fasta-utils

Set of tools to manipulate and compute statistics on FASTA files

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

fastq-qual-stats

Tool that computes statistics on sequencing data.

fastq-sample

fetch-cscg

filter-reads

functionnalannotation

gtdbtk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

jellyfish

A fast multi-threaded k-mer counter

kmc

Fast and frugal disk based k-mer counter

kraken

Kraken taxonomic sequence classification system

merge-cdhit-clusters

metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

mgs-canopy-algorithm

Fork of the canopy clustering algorithm of Nielsen et al.

mgs-scripts

motus

motus - a tool for marker gene-based OTU (mOTU) profiling

panphlan

PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples

pb-metagenomics-tools

pb-metagenomics-tools