Sailfish protocols

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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 pipelines

 (7)
2017
PMCID: 5709755
PMID: 28960191
DOI: 10.1038/bcj.2017.86

[…] from mds (aml-mds). patients were consented and studies were approved by the bc cancer agency research ethics board under protocol number h13-02687. expression quantification was performed using sailfish (version 0.9.0) to generate raw read counts and transcripts-per-million expression measures. variant-calling was performed on gene targets with known relevance to myeloid malignancies using […]

2016
PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] of rna-seq is to estimate gene and transcript expression. this application is primarily based on the number of reads that map to each transcript sequence, although there are algorithms such as sailfish that rely on k-mer counting in reads without the need for mapping []. the simplest approach to quantification is to aggregate raw counts of mapped reads using programs such as htseq-count [] […]

2016
PMCID: 5103334
PMID: 27832764
DOI: 10.1186/s12864-016-3227-8

[…] h. sapiens, s. scrofa and b. taurus were retrieved using the ensembl web-tool biomart []. for each library (nbat = 4, nhuman = 6, npig = 3, ncow = 1), these orthologous genes were quantified using sailfish (v0.7.6) with the default parameters []. the raw count of each gene in each library was collected and the genes that were not expressed in any libraries were excluded from de gene analysis. […]

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, followed by deseq to assess differential expression. as expected, the data obtained for the 3 wt md cells clustered strongly together while the 4 […]

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

[…] the genome-wide analyses of pre-mrna splicing was done using suppa. this method generated a list of splicing events from the mm10 annotation and then used the transcript quantification from sailfish to calculate the psi value for each splicing event (or transcript isoform) for each rna-seq data. we only used transcripts with a level of expression (transcript per million tpm) above 1. […]


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Sailfish in publications

 (27)
PMCID: 5809388
PMID: 29434199
DOI: 10.1038/s41467-018-02866-0

[…] types of “protein_coding” were selected as histone-coding genes. heat maps were generated using “aheatmap” function in the “nmf” r package. tpm values for each transcript were quantified using the sailfish (version 0.9.2) “quant” command with the parameter “-l u.”, transcript-level expression levels were quantified in the unit of count or tpm using the sailfish “quant” command […]

PMCID: 5815852
PMID: 29400649
DOI: 10.7554/eLife.30842.031

[…] were used., the grcm38.p5 (genome reference consortium mouse reference 38) assembly was used for all mouse data, and the set of annotated repeat types was taken from the repbase database (). sailfish version 0.6.3 aligner was used to quantify the abundance of previously annotated rna transcripts from rna-seq data (). analyses were performed with a modified k-mer size of k = 17 and used […]

PMCID: 5725498
PMID: 29229905
DOI: 10.1038/s41467-017-02305-6

[…] rna-sequencing data is the presence of multi-mapped (or ambiguous) reads. currently, there are many different bioinformatic strategies that can be used to align (e.g., star, tophat, bowtie, salmon, sailfish, etc.) and quantify scrna-seq data (e.g., htseq, cufflinks, salmon, sailfish, etc.)., however, independent of the method applied, one of two possible strategies can be used to align reads, […]

PMCID: 5709755
PMID: 28960191
DOI: 10.1038/bcj.2017.86

[…] from mds (aml-mds). patients were consented and studies were approved by the bc cancer agency research ethics board under protocol number h13-02687. expression quantification was performed using sailfish (version 0.9.0) to generate raw read counts and transcripts-per-million expression measures. variant-calling was performed on gene targets with known relevance to myeloid malignancies using […]

PMCID: 5547501
PMID: 28784092
DOI: 10.1186/s12864-017-4002-1

[…] explain the observed reads with a minimum number of isoforms. the strategy is similar to one iteration of the em algorithm used in rsem []., most recently, ultra-fast alignment-free methods, such as sailfish [], salmon [] and kallisto [], have been developed by exploiting the idea that precise alignments are not required to assign reads to their origins. kallisto introduced a de bruijn graph […]


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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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