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fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
dbmi-bgm / granite
Forked from bgm-cwg/novoCallerA collection of software to work with genomic variants
A curated list of awesome nanopore analysis tools.
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.
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"
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.