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adapterremoval

AdapterRemoval v2 - rapid adapter trimming, identification, and read merging

admixtools

Tools test whether admixture occurred and more

ale

Assembly Likelihood Estimator

alphafold

Open source code for AlphaFold.

anvio

An analysis and visualization platform for 'omics data

augustus

Genome annotation with AUGUSTUS

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

bcalm

compacted de Bruijn graph construction in low memory

beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees

blight

De Bruijn graph representation in low memory

cenote-taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs

chewbbaca

BSR-Based Allele Calling Algorithm

confindr

Intra-species bacterial contamination detection

copla

A taxonomic classifier of plasmids

crass

The CRISPR assembler

ete

ETE is a Python programming toolkit for building, comparing, annotating, manipulating and visualising trees. It provides both a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

funguild

FUNGuild: parsing OTUs into functional guilds

fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data

gitcheck

Check multiple git repository in one pass / Vérifiez vos dépôt git en une seule passe

hgtector

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

hisat2

Graph-based alignment (Hierarchical Graph FM index)

illumina-utils

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).

kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

kaptive

kleborate

kmc

Fast and frugal disk based k-mer counter

kraken

Kraken taxonomic sequence classification system

kraken2

The second version of the Kraken taxonomic sequence classification system

logstash

logstash - transport and process your logs, events, or other data

logstash_filter_ldapresolve

LDAPresolve filter will add to the event the fields 'login', 'user' and 'group' based on LDAP request with provided uidNumber information.