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1brc

1️⃣🐝🏎️ The One Billion Row Challenge -- A fun exploration of how quickly 1B rows from a text file can be aggregated with Java

affinity-propagation-sparse

Affinity Propagation with Sparse Similarities

aligngraph2

Similar genome assisted reassembly pipeline for PacBio long reads

assisi

A somatic mutation signature simulator

bam-matcher

bamcov

BASH logic for generating a coverage-reduced BAM file

bammer

QC methods for checking if two BAM files from the same sample

bazam

A read extraction and realignment tool for next generation sequencing data

bed2vcf

Convert a BED file (and a FASTA reference) to *mostly* valid VCF.

bedtools

A powerful toolset for genome arithmetic.

bh20-workflows-bhxiv

Workflows topic group BioHackathon 2020 mini-publication for https://BioHackrXiv.org

bindash

Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop

bio_docker

Dockerfiles for several SV callers and other miscellaneous bio apps.

bioicons

A library of free open source icons for science illustrations in biology and chemistry

biosandbox

Tools, scripts and programs for playing with biological data

biowulf-scripts

Scripts I use for analysis on NIH's Biowulf system.

bitarray

C bit array structs and methods

brass

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements.

breakmer

A method to identify structural variation from sequencing data in target regions

bsort

Extremely fast inplace radix sort

bwa-0.7.10

Reference bwa aln implementation for Agave API

bwamem2-bwakit-nf

bwa-mem2 + bwakit mapping flow

cacao

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

canu

A single molecule sequence assembler for genomes large and small.

cbitset

A simple bitset library in C

cgpbox

Core calling tools in a convenient docker image

cgranges

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

check-sex

Determine the biological sex of a human whole-genome BAM file

claragenomicsanalysis

SDK for GPU accelerated genome assembly and analysis

cloudmarker

Cloud monitoring tool and framework