SSAHA protocols

SSAHA specifications

Information


Unique identifier OMICS_00690
Name SSAHA
Alternative name Sequence Search and Alignment by Hashing Algorithm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Roche
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Zemin Ning <>
  • person_outline James Mullikin <>

Publication for Sequence Search and Alignment by Hashing Algorithm

SSAHA IN pipelines

 (13)
2017
PMCID: 5391098
PMID: 28406973
DOI: 10.1371/journal.pone.0175729

[…] from the dataset before mapping if they did not contain the rep-235 sequence in order to remove artificial constructs., in the next step, the pseudoreads were mapped to the tre5-absr sequence using ssaha [25] to determine the tre5-absr-derived part of the reads. based on this mapping the retrotransposon-derived part of the reads was trimmed using an in-house script. to trim the trna gene part […]

2015
PMCID: 4325683
PMID: 25698879
DOI: 10.4137/BBI.S20751

[…] (genome or transcriptome) by screening ngs data with the blast-like alignment tool blat24 for adapter sequence removal, quality score determination by fast quality control fastqc,25 and mapping with sequence search and alignment by hashing algorithm 2 ssaha2.26 the pipeline parses genomic data provided in genbank format to internally construct an annotated genome divided in watson and crick […]

2015
PMCID: 4495061
PMID: 26151830
DOI: 10.1371/journal.pone.0132120

[…] of all 15mers forming a probe were analyzed. the average 15mer frequency was computed, and only probes having less than a 100-fold frequency were used. uniqueness of the probes was determined by the sequence search and alignment by hashing algorithm (ssaha) program [61] developed at the sanger institute (http://www.sanger.ac.uk/resources/software/ssaha/). ssaha probes were compared […]

2015
PMCID: 4495061
PMID: 26151830
DOI: 10.1371/journal.pone.0132120

[…] 15mer frequency was computed, and only probes having less than a 100-fold frequency were used. uniqueness of the probes was determined by the sequence search and alignment by hashing algorithm (ssaha) program [61] developed at the sanger institute (http://www.sanger.ac.uk/resources/software/ssaha/). ssaha probes were compared to the reference genome from which they were generated (maize […]

2015
PMCID: 4495061
PMID: 26151830
DOI: 10.1371/journal.pone.0132120

[…] uniqueness of the probes was determined by the sequence search and alignment by hashing algorithm (ssaha) program [61] developed at the sanger institute (http://www.sanger.ac.uk/resources/software/ssaha/). ssaha probes were compared to the reference genome from which they were generated (maize genome agp v1, release 4a53; www.maizesequence.org). for each oligonucleotide, mapping determined […]

SSAHA institution(s)
Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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