SeqMonk protocols

View SeqMonk computational protocol

SeqMonk statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Differential expression DNA methylation visualization Known transcript quantification Quantitative score assessment Read alignment visualization chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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

Versioning


Add your version

Maintainer


  • person_outline Simon Andrews <>

SeqMonk in pipelines

 (50)
2018
PMCID: 5836094
PMID: 29444933
DOI: 10.15252/embr.201744957

[…] sequence data were processed by standard illumina pipelines. the sr reads were mapped to mm9 or te consensus sequence by bowtie after adapter trimming by cutadapt. the aligned reads were analyzed by seqmonk and excel., ep‐cam‐positive germ cells from testes of 10‐day‐old mice were sorted by bd facsaria™ iiu (bd biosciences), and bisulfite analysis was performed as described previously . pcr […]

2018
PMCID: 5906632
PMID: 29670118
DOI: 10.1038/s41467-018-03904-7

[…] library quality was analyzed on a bioanalyzer. high-throughput sequencing was performed on the hiseq 2500 (illumina)., quality control of the rna-seq raw files was performed using rseqc software and seqmonk (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). this was followed by mapping to mm9 genome assembly using star aligner. reads with more than two mismatches were filtered […]

2018
PMCID: 5909736
PMID: 29505958
DOI: 10.1016/j.neo.2018.01.009

[…] reads along mrna features as a basis of quantification. differentially expressed genes (deg) were identified as showing significant changes by either deseq2 or intensity difference testing (seqmonk) algorithms (p<0.005) between wnt3a/rspo2 treated and control sample sets, and having a fold difference of minimum 1.3. rna sequencing data is available from the european nucleotide […]

2017
PMCID: 5370449
PMID: 28351387
DOI: 10.1186/s13059-017-1187-1

[…] trimmed sequences were aligned using bismark [] (v0.16.3). methylation calls were extracted after duplicate sequences had been excluded. data visualization and analysis were performed using seqmonk and custom rstudio scripts. data from replicates of the same condition were merged using seqmonk’s data group option, in order to enhance coverage and detection of subtle differences. […]

2017
PMCID: 5370449
PMID: 28351387
DOI: 10.1186/s13059-017-1187-1

[…] (v1.2, parameters: view -f 0x100 -b –h). peak calling was performed using macs2 [] (v2.1.1, parameters: callpeak -g hs –n test –b –q 0.01). data visualization and mapping to cgis was performed using seqmonk and custom rstudio., to identify genes that showed consistent differential methylation across their gene body, we tested each gene for significant enrichment of overlapping dmrs compared […]


To access a full list of citations, you will need to upgrade to our premium service.

SeqMonk in publications

 (143)
PMCID: 5906632
PMID: 29670118
DOI: 10.1038/s41467-018-03904-7

[…] library quality was analyzed on a bioanalyzer. high-throughput sequencing was performed on the hiseq 2500 (illumina)., quality control of the rna-seq raw files was performed using rseqc software and seqmonk (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). this was followed by mapping to mm9 genome assembly using star aligner. reads with more than two mismatches were filtered […]

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

[…] with default settings. the trimmed reads were aligned by tophat () and further analyzed by cufflinks (). gene expression levels were plotted by cummerbund (http://compbio.mit.edu/cummerbund/), seqmonk, and custom r scripts. differentially expressed genes were identified by cummerbund., we thank p. w. faber of university of chicago genomics facility for facilitating sequencing […]

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 […]

PMCID: 5882937
PMID: 29615716
DOI: 10.1038/s41598-018-23653-3

[…] 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., differential expression analysis and generation […]

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

[…] reads were removed using the picard tools markduplicates software (http://broadinstitute.github.io/picard). resulting assemblies were visualized using a combination of circos, artemis, tablet, seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) software and custom r scripts making use of the rsamtools and gviz software packages., to confirm that enrichment for viral […]


To access a full list of publications, you will need to upgrade to our premium service.

SeqMonk review

star_border star_border star_border star_border star_border
star star star star star
Catherine SIRVEN's avatar image No country

Catherine SIRVEN

star_border star_border star_border star_border star_border
star star star star star
Desktop
Used it succesfully to visualise small RNA datasets.