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alpaca

A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.

astral

Accurate Species TRee ALgorithm

bioinformatics-training

Bioinformatics training resources

blobology

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED)

blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

catfasta2phyml

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

crossr

Compare transcriptomes from different species.

datol

Phylogenetic Marker Discovery Pipeline Utilizing Deep Sequencing Data

diamond

Accelerated BLAST compatible local sequence aligner.

fast-plast

Automated de novo assembly of whole chloroplast genomes.

fda-hive

FDA High-performance Integrated Virtual Environment (HIVE)

folioreaderkit

📚 A Swift ePub reader and parser framework for iOS.

iread

iRead is an EPUB reader for iOS written in Swift

kallisto

Near-optimal RNA-Seq quantification

loq_compliance_fda

mummer

Mummer alignment tool

mummer3

MUMmer3

novoplasty

NOVOPlasty - The organelle assembler and heteroplasmy caller

orthofinder

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

parsnp

pythondatasciencehandbook

Python Data Science Handbook: full text in Jupyter Notebooks

ragout

Chromosome assembly using multiple references

samsa

Programs and documentation for the SAMSA pipeline, version 1.0

samsa2

SAMSA pipeline, version 2.0. This version supports use on a local cluster using DIAMOND for annotations.

seq-gen

Sequence simulator

seqtk

Toolkit for processing sequences in FASTA/Q formats

sibelia

Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.

sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

subsystems

Code for making bioinformatics work with the SEED subsystems database a little easier.

training-material

A collection of Galaxy-related training material