Nils Homer

DWGSIM. Whole Genome Simulator for Next-Generation Sequencing

snakeparse. Making Snakemake workflows into full-fledged command line tools since 1999.

pbgzip. Parallel Block GZIP

fqme. Rust

TMAP. Torrent Mapping Alignment Program

samtools. C

basespace-invaders. A collection of tools to work with Illumina's basespace

gedmatch-tools. Tools and Python API for GEDMatch Genesis (https://genesis.gedmatch.com)

BFAST. BFAST: the Blat-like Fast Accurate Search Tool

snakemake-pytest. Snakemake with pytest example

callerpp. A simple consensus caller based on partial order alignment with spoa

rebgzf. Efficient gzip to BGZF transcoder using half-decompression (2-4x faster than decompress+recompress)

SRMA. Short-read Micro-Aligner

ksw. Ksw: (interactive) smith-waterman in C

bfx-qc-reporter. Bioinformatics QC Reporting Tools

read-structure-examples. Example Read Structures for BAM <-> FASTQ

flightmemory_exporter. PHP

bfx-examples. Bioinformatics Example Repository

ruamel_yaml_line_info. Line information for ruamel.yaml.

bioinformatic-worfklow-idioms. Common idioms and their implementation across Bioinformatic workflow languages

gget. gget enables efficient querying of genomic databases, such as Ensembl, UniProt, NCBI, directly into a Python or terminal programming environment. It was designed to support genomic data analysis.

euler. Solutions to http://projecteuler.net

DATA.

snakeskin. Making snakemake wrappers cool again

filesize. Large File Support Testing for Mac OS X Lion

bwa. Burrow-Wheeler Aligner

hapcut. program for haplotype phasing from sequence reads and related tools

pysam. Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

sga. experimental de novo sequence assembler using string graphs

homebrew. The missing package manager for OS X.

gatk. GATK Official Release Repository

awesome-pipeline. A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

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

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

airflow. Apache Airflow - A platform to programmatically author, schedule, and monitor workflows

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

badges. :pencil: Markdown code for lots of small badges :ribbon: :pushpin: (shields.io, forthebadge.com etc) :sunglasses:. Contributions are welcome! Please add yourse!