SAMBLASTER protocols

SAMBLASTER specifications

Information


Unique identifier OMICS_04682
Name SAMBLASTER
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format SAM
Output data The discordant read-pairs and/or split-read mappings used for structural variant calling.
Operating system Unix/Linux, Mac OS
Programming languages C++
License MIT License
Computer skills Advanced
Version 0.1.24
Stability Stable
Maintained Yes

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Publication for SAMBLASTER

SAMBLASTER IN pipelines

 (3)
2017
PMCID: 5241283
PMID: 28149306
DOI: 10.3389/fpls.2017.00012

[…] minlen:50 and mapped to the reference dh1 genome (iorizzo et al., 2016; ncbi accession lnrq01000000) using bwa-mem 0.7.12 (li and durbin, 2009). subsequently, duplicates were marked with samblaster 0.1.22 (faust and hall, 2014) and files were converted into bam and sorted using samtools 1.2 (li et al., 2009). snps were called using freebayes 1.0.1 (garrison and marth, 2012) […]

2017
PMCID: 5436647
PMID: 28545050
DOI: 10.1371/journal.pone.0176522

[…] and trim out illumina adaptor sequences. reads were aligned to the h37rv genome (genbank nc_000962) using the burrows-wheeler alignment algorithm version 0.5.7 [23], then sorted and indexed using samblaster [24]. variant calling was performed using freebayes version 0.9.14-18-g36789d8 [25]. freebayes parameters were set to assume a haploid organism and required a minimum alternate allele […]

2017
PMCID: 5548758
PMID: 28790370
DOI: 10.1038/s41598-017-06387-6

[…] reference sequence (build grch37) with novoalign (version 3.02.08). the aligned reads were sorted by base pair position and duplicates were marked using novosort. discordant reads were marked with samblaster (version 0.1.20) and sent to a separate file for manual inspection of breakpoints using the igv (version 2.3.61). svs were manually investigated using the igv by identifying peaks […]

SAMBLASTER institution(s)
Department of Biochemistry and Molecular Genetics and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
SAMBLASTER funding source(s)
Supported by NIH New Innovator Award (DP2OD006493-01) and a Burroughs Wellcome Fund Career Award.

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