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julia

The Julia Programming Language

DeepLabCut

Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

cdhit

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

raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible

graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

phylotree.js

Interactive viewer of phylogenetic trees

MitoZ

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes

nanopype

Snakemake pipelines for nanopore sequencing data archiving and processing

assembly-stats

Assembly statistic visualisation

graphmap2

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1

DBG2OLC

A genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.

REDItools

REDItools are python scripts to investigate RNA editing at genomic scale.

UniRep-analysis

Analysis and figure code from Alley et al. 2019.

hypo

HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies

estimate_genome_size.pl

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

ensembl-compara

The Ensembl Compara Perl API and SQL schema

pblat

parallelized blat with multi-threads support

pinfish

Tools to annotate genomes using long read transcriptomics data

ra

Assembler for raw de novo genome assembly of long uncorrected reads.

magicblast

booster

SwiftOrtho

A high performance tool to identify orthologs and paralogs across genomes.

doepipeline

A python package for optimizing processing pipelines using statistical design of experiments (DoE).

PyPore

A python tool box for fast and accurate quality control, conversion and alignment of nanopore sequencing data

FastqPuri

fastq quality assessment and filtering tool

stringtie2-initial-release

Transcript assembly and quantification for RNA-Seq

kodoja

Kodoja: identifying viruses from plant RNA sequencing data

clustermerge

Protein Clustering via Bottom-Up Merging

kmer-db