Sailfish pipeline

Sailfish specifications

Information


Unique identifier OMICS_03939
Name Sailfish
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A set of transcript and a set of reads.
Input format FASTA+FASTA,FASTQ
Operating system Unix/Linux, Mac OS
Programming languages C, C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.10.0
Stability Stable
Requirements C++11 conformant compiler, CMake
Maintained Yes

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Documentation


Maintainer


  • person_outline Carl Kingsford <>

Additional information


http://sailfish.readthedocs.io/en/master/

Publication for Sailfish

Sailfish IN pipeline

2016
PMCID: 5270529
PMID: 27763814
DOI: 10.1080/15476286.2016.1247148

[…] figure 4. , rna-seq analysis was performed for each rbm10 ko cell line and compared to the wt mandibular mepa cells that were analyzed in triplicate. gene expression analysis was performed using sailfish for mapping and transcript quantification,30 followed by deseq to assess differential expression.31 as expected, the data obtained for the 3 wt md cells clustered strongly together […]

Sailfish institution(s)
Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
Sailfish funding source(s)
Supported by National Science Foundation (CCF-1256087, CCF-1053918, and EF-0849899) and National Institutes of Health (1R21AI085376, 1R21HG006913, and R01HG007104).

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