SpeedSeq protocols

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SpeedSeq statistics

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SpeedSeq specifications


Unique identifier OMICS_04673
Name SpeedSeq
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes


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Publication for SpeedSeq

SpeedSeq in pipelines

PMCID: 5615344
PMID: 28837078
DOI: 10.3390/genes8090210

[…] insertion-deletion (indels) and single nucleotide variant (snvs) calling was performed using genome analysis tool kit (gatk) []. copy number variations (cnvs) were called using genome strip and speedseq software []. variants were filtered to detect rare potentially deleterious variants segregating with disease. rare deleterious snvs were extracted based on the frequency of alleles in 1000 […]

PMCID: 5100856
PMID: 27605517
DOI: 10.1534/g3.116.033902

[…] 300–400 bp, and 1965 gb of data were obtained. sequence reads were filtered for quality and then aligned to the mouse reference genome (grcm38/mm10) using the burrows–wheeler aligner implemented in speedseq software, which achieved at least 30× coverage for all lines ( and supplemental material, table s1)., private variants are line-specific variants., we used samtools/bcftools to call snps […]

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SpeedSeq in publications

PMCID: 5780461
PMID: 29362391
DOI: 10.1038/s41598-018-19782-4

[…] the umd3.1 assembly using bwa-mem with default options. summary statistics on coverage obtained and reads mapped per sire can be found in supplementary table . cnv calling was carried out based on speedseq, which incorporates lumpy and cnvnator for cnv detection. calls with length <1 kb or 1 mb were excluded. in accordance with the application guidelines, a q0-filter of 0.5 for cnvnator […]

PMCID: 5727227
PMID: 29234127
DOI: 10.1038/s41598-017-17802-3

[…] to the presence of background virus diversity., for detection of recombination breakpoints, cleaned data from each sample ngs library were individually aligned to the vdv1 and dwv references using speedseq (version 0.1.2). structural variants were detected using the lumpy smooth script from the lumpy package (version 0.2.13) and additional genotype and coverage metrics for each variant […]

PMCID: 5701507
PMID: 29178945
DOI: 10.1186/s13059-017-1354-4

[…] are listed in additional file : tables s2 and s3., wgs was carried out using illumina hiseq x ten at mean coverages of 20×. qualified reads were mapped to the mouse reference genome (mm10) by speedseq [] (https://github.com/hall-lab/speedseq) with default parameters. freebayes (v0.9.10) [] and lumpy [] (https://github.com/arq5x/lumpy-sv) were run on the aligned sequence files (bam files) […]

PMCID: 5666005
PMID: 29093439
DOI: 10.1038/s41467-017-01174-3

[…] at 2 and multiplied around the 2-axis to maximize number of genes near (within 0.1) of 1, 3, and 4 (to adjust for normal contamination)., wgs dna sequences were aligned to hg19 using bwa mem using speedseq. snvs and indel variants were identified using freebayes on each patient (see code repository for parameters). variants were annotated using snpeff and variants with quality below 5 […]

PMCID: 5532773
PMID: 28750619
DOI: 10.1186/s12917-017-1144-y

[…] instrument with 350 to 550 bp pcr-free libraries to 150 bp read length. the sequence data for each cat were aligned to the chromosomes of the domestic cat reference assembly (felis catus 8.0) using speedseq []. variants, specifically snvs and small indels (<10 bp), were called using the genome analysis toolkit (gatk) haplotypecaller and genotypegvcfs []. samtools flagstat [] and gatk […]

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SpeedSeq institution(s)
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA; Utah Science Technology and Research (USTAR) Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA; Wellcome Trust Sanger Institute, Hinxton, UK; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA

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