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Sra-tools
Jul 20, 2023
NCBI’s toolkit for handling data in INSDC Sequence Read Archives
SRA tools is a toolkit for using data in the INSDC Sequence Read Archives.
SRAs operated by International Nucleotide Sequence Database Collaboration houses sequence reads and alignments generated by “next-gen” sequencers. SRA tools allows conversion of .sra files, which INSDC SRAs maintain, from/to other formats that the ‘next-gen’ sequenecers generate including
- csfasta/csqual ABI SOLiD
- fastq and fasta for writing
- hdf5 PacBio, reading only
- qseq older Illumina
- sam writing only / bam reading only
- sff
The toolkit uses NCBI-VDB back-end enabling seamless access to remote SRA data and local SRA files.
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