nh13

ped-sim

Pedigree simulator

thesis

my PhD thesis

kraken2

The second version of the Kraken taxonomic sequence classification system

snakeparse

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

sample-sheet

Parse Illumina sample sheets with Python

Basecalling-comparison

A comparison of different Oxford Nanopore basecallers

bfx-qc-reporter

Bioinformatics QC Reporting Tools

UK_Biobank_GWAS

Overview of the data QC, code, and GWAS summary output from the 2017 UK Biobank data release

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

sircel

Identify cell barcodes from single-cell genomics sequencing experiments

maf-lib

Python package for processing and creating MAF files for the GDC

erccdashboard

This is the git repository for erccdashboard on Bioconductor. Contributions: http://www.nist.gov/mml/bbd/erccdashboard.cfm, https://github.com/usnistgov/erccdashboard, http://tinyurl.com/erccsrm. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=erccdashboard. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/erccdashboard

hapcut2

Performs haplotype assembly from genomic DNA sequence reads for a single individual using a maximum-likelihood based approach. Performs well on diverse NGS technologies, including long read data and Hi-C.

hapcut

program for haplotype phasing from sequence reads and related tools

hapcut

program for haplotype phasing from sequence reads and related tools

rtg-tools

RTG Tools: Utilities for accurate VCF comparison and manipulation

vg

tools for working with genome variation graphs

stringmetric

:dart: String metrics and phonetic algorithms for Scala (e.g. Dice/Sorensen, Hamming, Jaccard, Jaro, Jaro-Winkler, Levenshtein, Metaphone, N-Gram, NYSIIS, Overlap, Ratcliff/Obershelp, Refined NYSIIS, Refined Soundex, Soundex, Weighted Levenshtein).

fgbio

Tools for working with genomic and high throughput sequencing data.

dagr

A scala based DSL and framework for writing and executing bioinformatics pipelines as Directed Acyclic GRaphs

JeanLuc

speedseq

A flexible framework for rapid genome analysis and interpretation

elasticluster

Create clusters of VMs on the cloud and configure them with Ansible.

hap.py

Haplotype VCF comparison tools

ArnoldC

Arnold Schwarzenegger based programming language

rawls

Rawls service for DSDE

herc

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

DATA

bioruby-gag

bio-gag is a biogem for detecting and correcting a particular type of error (gag errors) that occurs/occurred in a particular version of the IonTorrent sequencing kit.