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atlas

ATLAS - Three commands to start analysing your metagenome data

atom

:atom: The hackable text editor

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

biocode

Bioinformatics code libraries and scripts

biopython.github.io

Source of biopython.org website, migrated from MediaWiki

breakdancer

SV detection from paired end reads mapping

cat

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

ccmetagen

Microbiome classification pipeline

cdna_cupcake

Miscellaneous collection of Python and R scripts for processing sequencing data

crisprcasidentifier

Machine learning for accurate identification and classification of CRISPR-Cas systems

crispridentify

data-science-from-scratch

code for Data Science From Scratch book

entap

Eukaryotic Non-Model Transcriptome Annotation Pipeline - Latest Release v0.9.2

fastp

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

fuento

Fuento is a functional enrichment tool for bioinformatic analysis.

ggsashimi

Command-line tool for the visualization of splicing events across multiple samples

hemberg-scrna-seq-course

interactivenn

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

isoseq-3.0

User Documentation

isoseq_sa3nup

Documentation and Developers Code Base for Iso-Seq SMRTAnalysis 3.x and beyond

jgi-query

A simple command-line tool to download data from the Joint Genome Institute's database

long-read-assembler-comparison

Benchmarking of long-read assembly tools for bacterial whole genomes

lstrap

metameta

minimap2_freebayes

Problems running Freebayes from Minimap2 Alignments-Pacbio reads

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

oneliners

Useful bash one-liners for bioinformatics.

opera-ms

OPERA-MS - Hybrid Metagenomic Assembler

opfi

A Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets.

orthofinder

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"