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SFA-SPA specifications


Unique identifier OMICS_07617
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Shibu Yooseph <>

Publication for SFA-SPA

SFA-SPA in pipeline

PMCID: 4939949
PMID: 27400380
DOI: 10.1371/journal.pcbi.1004991

[…] well with the query, which may be redundant. therefore, we recommend using other de novo assembly programs to further refine the set of output contigs (e.g. spades [] for nucleotide assembly and sfa-spa [] for protein assembly). in summary, the hmm-graspx based mg/mt analysis pipeline allows for estimation of gene/transcript abundances and targeted reconstruction of both protein […]

SFA-SPA in publication

PMCID: 4939949
PMID: 27400380
DOI: 10.1371/journal.pcbi.1004991

[…] short peptide reads are recruited by mapping all reads to the verified contigs that are generated in the previous step., targeted protein assembly can be performed using peptide assembler (e.g. sfa-spa []) on hmm-graspx recruited short peptides., targeted nucleotide assembly can be performed using nucleotide assembler (e.g. spades []) on the original nucleotide sequences that correspond […]

SFA-SPA institution(s)
Informatics Department, J Craig Venter Institute, La Jolla, CA, USA

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