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SeqMonk specifications


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


No version available


  • person_outline Simon Andrews

SeqMonk citations


Global H3.3 dynamic deposition defines its bimodal role in cell fate transition

Nat Commun
PMCID: 5906632
PMID: 29670118
DOI: 10.1038/s41467-018-03904-7

[…] Quality control of the RNA-Seq raw files was performed using RSeQC software and SeqMonk ( This was followed by mapping to mm9 genome assembly using STAR aligner. Reads with more than two mismatches were filtered out and […]


Low input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex

Sci Adv
PMCID: 5906078
PMID: 29675472
DOI: 10.1126/sciadv.aar8187

[…] alore! with default settings. The trimmed reads were aligned by TopHat () and further analyzed by cufflinks (). Gene expression levels were plotted by CummeRbund (, SeqMonk, and custom R scripts. Differentially expressed genes were identified by CummeRbund. […]


Transient reduction of DNA methylation at the onset of meiosis in male mice

PMCID: 5883305
PMID: 29618374
DOI: 10.1186/s13072-018-0186-0

[…] Individual chromosomes were analyzed separately (extracted from sorted BAM files). Biological replicates were analyzed separately for independent assessment. The files were uploaded into SeqMonk and read coverage was quantitated in the following manner: running, non-overlapping window probes of 5 kb were created to span the chromosome length. Read counts (the probes) were quantitated […]


A multi step transcriptional cascade underlies vascular regeneration in vivo

Sci Rep
PMCID: 5882937
PMID: 29615716
DOI: 10.1038/s41598-018-23653-3
call_split See protocol

[…] tation release 84 was used to identify genes, transcripts, protein-coding transcripts, exons, and rRNA for feature counting. Feature counts corrected for genomic DNA contamination were obtained using SeqMonk,; read counts for genes were determined as counts mapped to the union of all exons for all transcript isoforms of a given gene. […]


A spliced latency associated VZV transcript maps antisense to the viral transactivator gene 61

Nat Commun
PMCID: 5862956
PMID: 29563516
DOI: 10.1038/s41467-018-03569-2

[…] licate reads were removed using the Picard Tools MarkDuplicates software ( Resulting assemblies were visualized using a combination of Circos, Artemis, Tablet, SeqMonk ( software and custom R scripts making use of the Rsamtools and Gviz software packages.To confirm that enrichment for viral nucleic a […]


Comparison of whole genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

Genome Biol
PMCID: 5856372
PMID: 29544553
DOI: 10.1186/s13059-018-1408-2
call_split See protocol

[…] After processing with Bismark, read coverage depth was analysed with SeqMonk []. Custom genomes were created for mtDNA, satellite repeat and M13, and the reads were aligned preserving the strand information. Because of its repetitive nature, the data for major satellit […]


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Anonymous user #22273's avatar image No country

Anonymous user #22273

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Used it succesfully to visualise small RNA datasets.