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ropebwt

ropebwt2

Incremental construction of FM-index for DNA sequences

ropebwt3

Construction and utility of BWT for DNA string sets

rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

rtgeval

Wrapper for RTG's vcfeval; DEPRECATED!

samblaster

samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.

samtools

This is *NOT* the official repository of samtools.

samtools-legacy

For testing only. DON'T USE!

schemas

The upstream repo has been deprecated, so is this one.

sdg

EXPERIMENTAL implementation of side graph

sdust

Symmetric DUST for finding low-complexity regions in DNA sequences

seqtk

Toolkit for processing sequences in FASTA/Q formats

sff2fastq

extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output

sgdp-fermi

FermiKit small variant calls for public SGDP samples

smtl-paper

Samtools statistics paper (Li, 2011)

srf

SRF: Satellite Repeat Finder

tabtk

Toolkit for processing TAB-delimited format

thesis

PhD thesis

treebest

TreeBeST: Tree Building guided by Species Tree

trf-mod

Tandem Repeats Finder: a program to analyze DNA sequences

trimadap

Fast but inaccurate adapter trimmer for Illumina reads

unicall

A wrapper for calling small variants from human germline high-coverage single-sample Illumina data

unimap

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

varcmp

The first CHM1 paper (Li, 2014)

wgsim

Reads simulator

wise3

The 3rd incarnation of the Wise package for sequence analysis

wtdbg2

Not my work; for creating PRs only

yak

Yet another k-mer analyzer

zenodo-upload

upload big files to Zenodo using cURL, jq and bash