Jul 20, 2023

High-performance read alignment, quantification and mutation discovery

The Subread package comprises a suite of software programs for processing next-gen sequencing read data including

Subread a general-purpose read aligner which can align both genomic
DNA-seq and RNA-seq reads. It can also be used to discover genomic
mutations including short indels and structural variants.

Subjunc a read aligner developed for aligning RNA-seq reads and for the
detection of exon-exon junctions. Gene fusion events can be detected as

featureCounts a software program developed for counting reads to genomic
features such as genes, exons, promoters and genomic bins.

Sublong a long-read aligner that is designed based on seed-and-vote.

exactSNP a SNP caller that discovers SNPs by testing signals against local
background noises.

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