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bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

bioconda-recipes

Conda recipes for the bioconda channel.

captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

captus.docs

Documentation and tutorials for Captus: https://github.com/edgardomortiz/Captus

ddrad_tools

A collection of tools designed for working with ddRAD data.

discovista_astral-pro

fineradstructure-tools

Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)

hybpiper

Recovering genes from targeted sequence capture data

ipyrad

Interactive assembly and analysis of RAD-seq data sets

nanoamp

Species identification via Nanopore sequencing of barcoded amplicons

paralog-finder

Detects and blacklists paralog RAD loci analyzed in Stacks or ipyrad, based on the McKinney 2017 method (doi:10.1111/1755-0998.12613)

pyrad

Modifed version of pyrad to finish large assemblies from ipyrad that are stuck in step 6

rad-gatk

Tools to obtain locus-based statistics from RADseq data analyzed with GATK

radscripts

sam2consensus

Get the consensus sequences from SAM (and BAM) files, ignoring the reference

shotgun2rad

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis