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cat

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

catfasta2phyml

Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file

cd_rf_microbiome

Scripts for processing and analyzing the microbiome data associated with the manuscript "Multi-omics Differentially Classify Disease State and Treatment Outcome in Paediatric Crohn’s Disease"

cdhit

Automatically exported from code.google.com/p/cdhit

cenote-taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs

cgview

CGView is a Java package for generating high-quality, zoomable maps of circular genomes.

checkm

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

cherry

Host prediction

classifier

RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s

co-occurrence

R scripts for performing co-occurrence analyses

coelho2021_gmgcv1

common_used_bash

community-assembly-processes-and-species-coexistences-of-agricultural-soils-microbiome

complexheatmap

Make Complex Heatmaps

concoct

Clustering cONtigs with COverage and ComposiTion

conda-docs

Conda documentation

coverm

Read coverage calculator for metagenomics

cowplot

crisprcasfinder

A Perl script allowing to identify CRISPR arrays and associated Cas proteins from DNA sequences

crispridentify

crispropendb

csvtk

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

d3

Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

das_tool

DAS Tool

dataviz

A book covering the fundamentals of data visualization

deblur

Deblur is a greedy deconvolution algorithm based on known read error profiles.

deepvirfinder

Identifying viruses from metagenomic data by deep learning

demovir

Taxonomic classification of viruses at Order and Family level

diamond

Accelerated BLAST compatible local sequence aligner.