SeqMonk pipeline

SeqMonk specifications

Information


Unique identifier OMICS_01936
Name SeqMonk
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 0.32.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Simon Andrews <>

SeqMonk IN pipelines

 (37)
2017
PMCID: 5554778
PMID: 28768204
DOI: 10.1016/j.celrep.2017.07.009

[…] and was filtered to remove non-primary alignments or alignments with mapping quality (mapq) < 20. mapped rna-seq data were quantitated using the rna-seq quantitation pipeline in seqmonk software (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). genome version used was mus musculus grcm38 (08/06/2012)., cells annotated as triplets, multiples, or empty wells […]

2017
PMCID: 5554778
PMID: 28768204
DOI: 10.1016/j.celrep.2017.07.009

[…] or alignments with mapping quality (mapq) < 20. mapped rna-seq data were quantitated using the rna-seq quantitation pipeline in seqmonk software (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). genome version used was mus musculus grcm38 (08/06/2012)., cells annotated as triplets, multiples, or empty wells were filtered out. cells expressing fewer than 4,000 genes […]

2017
PMCID: 5738345
PMID: 29263336
DOI: 10.1038/s41598-017-18091-6

[…] the ion proton sequencing were trimmed for adapter-sequences using cutadapt56 and aligned to the human reference genome hg19 with bwa57. alignments were generated in bam format and uploaded to the seqmonk software (http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/). the datastore summary report from seqmonk provides information about the analysed data stores (supplementary table s1). […]

2016
PMCID: 4721952
PMID: 26796638
DOI: 10.1371/journal.pgen.1005762

[…] a maximum of 2 mismatches. reads that did not align to the genome were then aligned to the lister427 vsgnome (http://129.85.245.250/index.html) using the same parameters. reads were quantified using seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk) from babraham bioinformatics or, in the case of vsg aligned reads, custom python scripts., for the plots shown in fig 6, log2(rpkm) […]

2016
PMCID: 4721952
PMID: 26796638
DOI: 10.1371/journal.pgen.1005762

[…] genome were then aligned to the lister427 vsgnome (http://129.85.245.250/index.html) using the same parameters. reads were quantified using seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk) from babraham bioinformatics or, in the case of vsg aligned reads, custom python scripts., for the plots shown in fig 6, log2(rpkm) values for each gene were included in the analysis […]

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