SeqMonk specifications


Unique identifier OMICS_01936
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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  • person_outline Simon Andrews <>

SeqMonk citations

PMCID: 5541547

[…] genes with no or very low read counts (considered as noise in seqmonk) to avoid bias in the data that might skew the analysis. the raw read counts table and quantitated genes report (fpkm values) of seqmonk analysis were exported to excel (microsoft) and further analysed. moreover, for b. mori, as the gff file from ensembl was not annotated with the chromosome number, which is required […]

PMCID: 4928930

[…] coordinates of the intergenic regions and information on the flanking genes were obtained from the saccharomyces genome database using the yeastmine tool. this information was loaded into seqmonk as an annotation set and was used to generate 6303 intergenic probes. subsequently, each of these probes were tiled in contiguous sections of 50 nt. this generated a total number of 65198 […]

PMCID: 4721952

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

PMCID: 4581735

[…] (european nucleotide archive accession numbers ae003852.1and ae003853.1) using bowtie2 [47]. mapped reads were visualized using seqmonk v2.8 (babraham bioinformatics) and read counts obtained using seqmonk’s rna-seq quantitation pipeline. statistical analysis for differentially expressed genes was performed using the deseq package [48] and genes with > 2 fold change and p-value <0.05 […]

PMCID: 4572612

[…] the saha used for our first experiments, samuel clokie, wmrgl, for assistance with hi-seq dna sequencing and simon andrews and the bioinformatics team at the babraham institute for introducing us to seqmonk. we thank peter cockerill, padma-sheela jayaraman and karl nightingale for critical reading of early versions of the manuscript. this work was supported by project grants from cancer research […]

SeqMonk review

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Catherine SIRVEN

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Used it succesfully to visualise small RNA datasets.

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