Find open-source science resources

GFF and GTF file manipulation and interconversion.

Suite of tools to handle gene annotations in any GTF/GFF format.

VCF manipulation and statistics (e.g. linkage disequilibrium, allele frequency, Fst).

A C++ library for parsing and manipulating VCF files.

Annotate a VCF with other VCFs/BEDs/tabixed files.

Telseq is a tool for estimating telomere length from whole genome sequence data.

Fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs.

Displaying sequence statistics for next-generation sequencing.

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

Automate common SAM & BAM conversions.

Collection of tools for working with BAM files.

structural variant calling and genotyping with existing tools, but,smoothly.

GRIDSS: the Genomic Rearrangement IDentification Software Suite.

Structural variant and indel caller for mapped sequencing data.

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

samtools/bcftools are a suite of tools for manipulating NGS data and can be used to call variants.

A polymorphic bayesian genotyping model with wide applicability.

Variant Discovery in High-Throughput Sequencing Data.

Bayesian haplotype-based polymorphism discovery and genotyping.

Deep learning-based variant caller

A software package for estimating gene and isoform expression levels from RNA-Seq data.

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.

Partial-Order Alignment for fast alignment and consensus of multiple homologous sequences.

An ultrafast protein aligner for `blastp` and `blastx` like searches.

A system for rapidly aligning entire genomes, whether in complete or draft form.

SIMD C library for global, semi-global, and local pairwise sequence alignments

the wavefront alignment algorithm (WFA) which expoit sequence similarity to speed up alignment

BWA-MEM drop-in replacement: 2-3x faster, 2-5x cheaper, 100% identical output on standard CPUs.

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Scalable gVCF merging and joint variant calling for population sequencing projects.

Scalable genomic analysis.

UNIX-style FASTA manipulation tools.

Toolkit for processing sequences in FASTA/Q formats.

file format conversion in Biopython in a convenient way.

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang.

Aggregate results from bioinformatics analyses across many samples into a single report.

FASTQ/A short-reads pre-processing tools: Demultiplexing, trimming, clipping, quality filtering, and masking utilities.

FASTQ and SAM quality control using Python.

A pipeline for preprocessing short and long sequencing reads, built with Nextflow.

Customizable pipeline for differential expression analysis with an intuitive GUI.

Batteries included genomic analysis pipeline for variant and RNA-Seq analysis, structural variant calling, annotation, and prediction.

A generic but comprehensive bacterial annotation pipeline, built with Nextflow, with nice graphical options for investigating results.

A flexible pipeline, built with Nextflow, for the complete analysis of bacterial genomes.

A list of pipeline resources.

Workflow standard developed by the Broad.

Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments.

Workflow library embedded in the Go programming language, focusing on supporting complex workflow constructs, compiling to a single binary, providing powerful file naming and comprehensive audit reports for every output

A python-based workflow manager.