fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

A collection of software to work with genomic variants

analysis pipeline for CODEC data

A curated list of awesome nanopore analysis tools.

Splits fastq files evenly

The second version of the Kraken taxonomic sequence classification system

Detect outlier long-reads by using its Illumina counterpart.

CLI tool to link methylation tags between two files

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

k-mer based assembly evaluation

The uncompromising Python code formatter

main repository for SMaHT pipelines

Haplotype VCF comparison tools

GTEx & TOPMed data production and analysis pipelines

Oxford Nanopore Technologies fast5 API software

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

LongQC is a tool for the data quality control of the PacBio and ONT long reads.

SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Mapped QC analysis program

A suite of tools for detecting expansions of short tandem repeats

Helper scripts for biological data processing from Sentieon

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

Distributed execution of bioinformatics tools on Apache Spark. Apache 2 licensed.