Musket protocols

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Musket specifications

Information


Unique identifier OMICS_01060
Name Musket
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Version 1.1
Stability Stable
Requirements
memusage
Maintained Yes

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Maintainer


  • person_outline Liu Yongchao <>

Publication for Musket

Musket in pipelines

 (4)
2018
PMCID: 5887026
PMID: 29622616
DOI: 10.1128/genomeA.00222-18

[…] paired-end protocol, leading to 1,409,297 read pairs (>120× average sequencing depth, ∼250 bp insert size)., sequenced reads were clipped and trimmed with alientrimmer () and corrected with musket (). the remaining processed reads were assembled and scaffolded with spades (). the draft genome has a total size of 3,255,527 bp, represented in 204 scaffolds, with an n50 value of 51,970 bp. […]

2017
PMCID: 5230755
PMID: 28081123
DOI: 10.1371/journal.pntd.0005216

[…] fastq files were performed with alientrimmer []. redundant or over-represented reads were reduced using the khmer software package (option:–c 70) []. finally, sequencing errors were corrected using musket [] and overlapping paired reads were merged with flash []. a de novo assembly was performed for each strain with the quality-filtered reads using spades v3.6 (options:-k […]

2017
PMCID: 5845742
PMID: 29099690
DOI: 10.1099/jmm.0.000622

[…] genetic analyses, reads were preprocessed to remove low quality sequences and library generation artifacts (e.g. adaptor contamination) with trimmomatic [], and base call errors were corrected with musket []. reads were then assembled de novo with spades []. the s. pyogenes genome is approximately 2 mbp in length. strains for which the de novo assembly was larger than 2.2 mbp were considered […]

2015
PMCID: 4433549
PMID: 25573702
DOI: 10.1093/aobpla/plu086

[…] by purification steps using dneasy (qiagen, venlo, the netherlands) according to . dna yield and quality were visually assessed on a 1 % agarose gel., the raw reads were error-corrected using musket (). this error-corrected set was used for the repeat assembly. prinseq-lite 0.20.04 () was used for quality control and filtering of reads (minimum read length of 50 nt, minimum average base […]


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Musket in publications

 (12)
PMCID: 5915733
PMID: 29691339
DOI: 10.1128/mBio.00573-18

[…] million read pairs per strain on average. statistics of assembly for all the isolates are summarized in ., all sequenced reads were clipped and trimmed with alientrimmer v.0.4.0 (), corrected with musket v.1.1 (), merged (if needed) with flash v.1.2.11 (), and subjected to a digital normalization procedure with khmer v.2.0 (). for each sample, processed reads were finally assembled with spades […]

PMCID: 5887026
PMID: 29622616
DOI: 10.1128/genomeA.00222-18

[…] paired-end protocol, leading to 1,409,297 read pairs (>120× average sequencing depth, ∼250 bp insert size)., sequenced reads were clipped and trimmed with alientrimmer () and corrected with musket (). the remaining processed reads were assembled and scaffolded with spades (). the draft genome has a total size of 3,255,527 bp, represented in 204 scaffolds, with an n50 value of 51,970 bp. […]

PMCID: 5723288
PMID: 29259619
DOI: 10.3389/fgene.2017.00180

[…] were eliminated by mapping to the chloroplast genome of sweet orange (bausher et al., ) and phix174 (nc_001422.1) with bwa (ver. 0.7.13) (li and durbin, ). the sequencing error was corrected with musket (ver. 1.0.6) (liu et al., ) to improve mapping quality at the default settings; next, all duplicated reads were excluded to retain unique sequencing reads. finally, adapter sequences […]

PMCID: 5737583
PMID: 29126189
DOI: 10.1093/gbe/evx229

[…] reads with over 30% poor quality bases (score below 20) were removed using two perl scripts (illuqc.pl and ambiguityfiltering.pl) included in the ngs qc tookit v2.3.3 package (). the software musket was used for error correction in the remaining reads (), and the tools fastuniq (for paired reads) and fastx_collapser (for unpaired reads) (http://hannonlab.cshl.edu/fastx_toolkit/; last […]

PMCID: 5563063
PMID: 28821237
DOI: 10.1186/s12859-017-1784-8

[…] error correction algorithms and implementations have been proposed for illumina data, including ace [], bayeshammer [], bfc [], bless [], bless 2 [], blue [], ec [], fiona [], karect [], lighter [], musket [], pollux [], quake [], quorum [], racer [], sga-ec [] and trowel []. for a comprehensive overview of the characteristics of these ec tools and those for other sequencing platforms, we refer […]


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Musket institution(s)
Institut fur Informatik, Johannes Gutenberg Universitat Mainz, Mainz, Germany; Department of Computing and Information Systems, The University of Melbourne, VIC, Australia

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