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adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

augustus

Genome annotation with AUGUSTUS

bamtools

C++ API & command-line toolkit for working with BAM data

basespace_clarity_lims

API libraries, application examples, and custom tools for BaseSpace Clarity LIMS

bedtools2

A powerful toolset for genome arithmetic.

bfx-qc-reporter

Bioinformatics QC Reporting Tools

bioawk

BWK awk modified for biological data

bstring

A fork of Paul Hsieh's Better String Library

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

clinicaldatasources

Open or Easy Access Clinical Data Sources for Biomedical Research

consensusfixer

Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.

cpython

The Python programming language

dcell

DCell browser and gene deletion simulator

deeptools

Tools to process and analyze deep sequencing data.

epic

Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.

fastai

The fast.ai deep learning library, lessons, and tutorials

fermikit

De novo assembly based variant calling pipeline for Illumina short reads

fgbio

Tools for working with genomic and high throughput sequencing data.

gemini

a lightweight db framework for exploring genetic variation.

giab_remap_38

Remap the Genome in a Bottle NA12878 validation variant calls to human genome build 38

hapdip

The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data

hibachi

Data simulation software that creates data sets with particular characteristics

htslib

C library for high-throughput sequencing data formats

interop

C++ Library to parse Illumina InterOp files

karyoploter

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

kat

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

lims2db

manta

Structural variant and indel caller for mapped sequencing data

mcfilterface

VCF file filtering pipeline

megaqc

Web application to collect and visualise data across multiple MultiQC runs.