SAMBLASTER protocols

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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

 (8)
2017
PMCID: 5241283
PMID: 28149306
DOI: 10.3389/fpls.2017.00012

[…] 50, leading:28, trailing:28, slidingwindow:10:28, minlen:50 and mapped to the reference dh1 genome (; ncbi accession lnrq01000000) using bwa-mem 0.7.12 (). subsequently, duplicates were marked with samblaster 0.1.22 () and files were converted into bam and sorted using samtools 1.2 (). snps were called using freebayes 1.0.1 () and filtered using vcffilter with parameters -f “qual > 20 […]

2017
PMCID: 5340393
PMID: 28267806
DOI: 10.1371/journal.pone.0173421

[…] 0.1.126) [], and the clean reads were aligned to the reference pig genome (sscrofa10.2) downloaded from ensemble (www.ensembl.org) with bwa mem (version:0.7.12) []. duplicated reads were marked with samblaster (version: 0.1.22) []. only the uniquely mapped (mapq ≥ 13) and non-duplicated alignments were used for peak calling. macs2 (version: 2.1.0.20150420) [] was employed to perform peak calling […]

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 [], then sorted and indexed using samblaster []. variant calling was performed using freebayes version 0.9.14-18-g36789d8 []. freebayes parameters were set to assume a haploid organism and required a minimum alternate allele fraction […]

2017
PMCID: 5499169
PMID: 28450459
DOI: 10.1534/genetics.116.198895

[…] sequence coverage from wgs of the clones was 97×. the reads were aligned against the genome sequence of saccer3 using burrows-wheeler aligner version 0.7.3 (). pcr duplicates were marked using samblaster version 0.1.22 (), and indels were realigned using gatk version 3.5 (). for single nucleotide variant (snv) and small indel analysis, variants were called using the bcftools call command […]

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 […]


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SAMBLASTER in publications

 (31)
PMCID: 5951856
PMID: 29760388
DOI: 10.1038/s41467-018-04008-y

[…] position based retrieval of reads was expedited and data storage requirements were minimized. next, to remove erroneous mutation calls due to pcr duplication, all duplicate reads were removed using samblaster. after removal of the duplicate reads, the base quality scores were recalibrated using the countcovariates and tablerecalibration tools included in the genome analysis toolkit software, […]

PMCID: 5922390
PMID: 29721196
DOI: 10.18632/oncotarget.24973

[…] approximately 300 million rna sequencing reads were generated for each tumor., dna sequencing data was aligned to grch37 (www.ncbi.nlm.nih.gov/assembly/2758/) by bwa [], duplicate-marked by samblaster [], and indel realignment and base quality recalibration performed by gatk v2.3 []. rna sequencing data is aligned by bowtie [] and rna transcript expression estimated by rsem []. tumor […]

PMCID: 5880256
PMID: 29602769
DOI: 10.1101/mcs.a002246

[…] reference genome (hg19) using bowtie2 (version 2.2.5) () and converted to bam format using samtools (version 0.1.19) (). duplicate reads were marked and removed from the resulting bam files using samblaster (version 0.1.21) ()., aligned reads were counted in 1000-bp windows across the entire genome using bedtools-2.25.0 (). coverage log ratios were calculated relative to a median reference […]

PMCID: 5880266
PMID: 29434027
DOI: 10.1101/mcs.a002618

[…] sequence alignments were refined according to community-accepted guidelines for best practices (https://www.broadinstitute.org/gatk/guide/best-practices). duplicate sequence reads were removed using samblaster-v.0.1.22, local realignment was performed on the aligned sequence data using the genome analysis toolkit (gatk) (v3.7–0), and churchill's own deterministic implementation of base quality […]

PMCID: 5873907
PMID: 29420191
DOI: 10.1534/g3.118.200021

[…] for balancers from stocks 504, 22239, 24759 and the hawley lab sm1 stock are described in ., breakpoints were identified as in . briefly, split and discordant read pairs were isolated using samblaster () from regions where rearrangements were previously reported to be present (). split and discordant pairs were then de novo assembled and blast was used to identify assembled fragments […]


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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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