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Sequence manipulation toolkit for FASTA/FASTQ files written in Nim.

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

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

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

A quality control tool for high throughput sequence data.

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

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

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

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

Prokka: rapid prokaryotic genome annotation. Prokka is one of the most cited annotation command line tools for microbial genome annotations.

A circos representation of multiple GWAS results.

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

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

file format conversion in Biopython in a convenient way.

A fuzzy Bruijn graph approach to long noisy reads assembly

Syntax Highlighting for Computational Biology file formats (SAM, VCF, GTF, FASTA, PDB, etc...) in vim/less/gedit/sublime.

Point and click, cross platform suite for analysing and visualizing next-generation sequencing datasets.

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

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