Jul 20, 2023

Pacific Biosciences patched and stripped down SeqAn

This is a public fork of the SeqAn Library v2.0.0, stripped down to just the header files and with a few custom fixes.

Some of PacBio’s tools depend on SeqAn for efficient implementations of some common data-structures for sequence analysis A huge thanks to SeqAn development team!. However PacBio only uses a small amount of the SeqAn code-base, and in addition requires a few minor fixes that didn’t make it in to the initial release of SeqAn v2.0.0. Thus to minimize confusion and band-width, we will depend on this fork instead of SeqAn proper.

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