github.com/Schaudge/hts@v0.0.0-20240223063651-737b4d69d68c/paper/paper.md (about)

     1  ---
     2  title: 'bíogo/hts: high throughput sequence handling for the Go language'
     3  tags:
     4    - bioinformatics
     5    - toolkit
     6    - golang
     7  authors:
     8   - name: R Daniel Kortschak
     9     orcid: 0000-0001-8295-2301
    10     affiliation: 1
    11   - name: Brent S Pedersen
    12     orcid: 0000-0003-1786-2216
    13     affiliation: 2
    14   - name: David L Adelson
    15     orcid: 0000-0003-2404-5636
    16     affiliation: 1
    17  affiliations:
    18   - name: School of Biological Sciences, The University of Adelaide
    19     index: 1
    20   - name: Department of Human Genetics, University of Utah
    21     index: 2
    22  date: 6 January 2017
    23  bibliography: paper.bib
    24  ---
    25  
    26  # Summary
    27  
    28  bíogo/hts provides a Go native implementation of the SAM specification [@SAMspec] for SAM and BAM alignment formats [@li] commonly used for representation of high throughput genomic data, the BAI, CSI and tabix indexing formats, and the BGZF blocked compression format. The bíogo/hts packages perform parallelized read and write operations and are able to cache recent reads according to user-specified caching methods. The parallelisation approach used by the bíogo/hts package is influenced by the approach of the D implementation, sambamba by Tarazov et al. [@tarasov].
    29  The bíogo/hts APIs have been constructed to provide a consistent interface to sequence alignment data and the underlying compression system in order to aid ease of use and tool development.
    30  
    31  # References