Jul 20, 2023

Collection of open source tools for genetic sequence analysis

The European Molecular Biology Open Software Suite EMBOSS is a comprehensive set about 100 of open source tools for genetic sequence analysis. EMBOSS is produced by the European Molecular Biology Network EMBnet - http//www.embnet.org/.

All EMBOSS tools are all built around the same set of core libraries - AJAX and NUCLEUS - and therefore share a unified user interface, have similar “look and feel”, and implement a uniform sequence addressing methodology.

The various components of EMBOSS are distributed under the GPL, except the core libraries which are under the LGPL.

EMBASSY packages are third party applications which have been integrated with the EMBOSS suite, but which are not included in the base EMBOSS distribution for licensing or other reasons. The EMBASSY packages live in the biology/embassy port.

Checkout these related ports:
  • Wise - Intelligent algorithms for DNA searches
  • Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
  • Vt - Discovers short variants from Next Generation Sequencing data
  • Vsearch - Versatile open-source tool for metagenomics
  • Viennarna - Alignment tools for the structural analysis of RNA
  • Velvet - Sequence assembler for very short reads
  • Vcftools - Tools for working with VCF genomics files
  • Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
  • Vcf2hap - Generate .hap file from VCF for haplohseq
  • Vcf-split - Split a multi-sample VCF into single-sample VCFs
  • Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
  • Unanimity - Pacific Biosciences consensus library and applications
  • Ugene - Integrated bioinformatics toolkit
  • Ucsc-userapps - Command line tools from the UCSC Genome Browser project
  • Trimmomatic - Flexible read trimming tool for Illumina NGS data