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lobSTR specifications

Information


Unique identifier OMICS_00109
Name lobSTR
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data One or more sequencing libraries.
Input format FASTA,FASTQ,BAM
Output data The alignment of STR reads and the most likely alleles for each STR locus.
Output format BAM+TSV
Operating system Unix/Linux
Programming languages C, C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 4.0.6
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Yaniv Erlich

Additional information


http://lobstr.teamerlich.org/documentation.html

Publication for lobSTR

lobSTR citations

 (35)
library_books

A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies

2018
Front Genet
PMCID: 5941971
PMID: 29770143
DOI: 10.3389/fgene.2018.00155

[…] tools to detect polymorphism of tr loci in raw reads from sequencing assays are among the most useful supporting tools/resources. examples of such data mining tools are: repeatseq (highnam et al., ) lobstr (gymrek et al., ), revister (tae et al., ), vntrseek (gelfand et al., ), myflq (van neste et al., ). pstr finder (lee et al., ), str-fm (fungtammasan et al., ), expansionhunter (dolzhenko et […]

library_books

Structural Basis for NusA Stabilized Transcriptional Pausing

2018
Mol Cell
PMCID: 5842316
PMID: 29499136
DOI: 10.1016/j.molcel.2018.02.008

[…] coli (e. coli) top10 strain (invitrogen). for recombinant protein expression, we constructed an e. coli strain, called lacr ii (low abundance of cellular rnases). lacr ii is derived from the e. coli lobstr strain () with additional rnase deletions to lower the amount of rnase contamination in purified protein samples (details to be published elsewhere); e. coli strain bl21(de3) rna- rnb- () […]

library_books

A microsatellite repeat in PCA3 long non coding RNA is associated with prostate cancer risk and aggressiveness

2017
Sci Rep
PMCID: 5715103
PMID: 29203868
DOI: 10.1038/s41598-017-16700-y

[…] the number, length and gc nucleotide composition of strs in the human genome from the repeatmasker library. polymorphic strs within the repeatmasker library were determined by screening against the lobstr program predicted strs that were carried out on the phase 1, 1000 genomes project datasets (1000genomes_phase_1.vcf.gz) from the willems et al. study using a custom perl script. essentially, […]

library_books

Profiling of Short Tandem Repeat Disease Alleles in 12,632 Human Whole Genomes

2017
Am J Hum Genet
PMCID: 5673627
PMID: 29100084
DOI: 10.1016/j.ajhg.2017.09.013

[…] some short indels in reads that span strs. other tools seek to identify str variants by specifically examining the sequencing reads that are piled around a target str region., a popular caller, lobstr, uses three separate steps: sensing, alignment, and allelotyping, which explicitly model two possible alleles (diploid) as well as sequencing errors typically associated with strs (because […]

library_books

Introducing site specific cysteines into nanobodies for mercury labelling allows de novo phasing of their crystal structures

2017
Acta Crystallogr D Struct Biol
PMCID: 5633906
PMID: 28994409
DOI: 10.1107/S2059798317013171

[…] mutants were generated using inverse pcr. the nb constructs contained an n-terminal pelb signal for secretion into the periplasm and a c-terminal 6×his tag. all nbs were expressed in e. coli lobstr cells (andersen et al., 2013) grown to an optical density of ∼0.6 before expression was induced with 0.2 mm iptg at 18°c overnight. cells were opened in lysis buffer [pbs buffer supplemented […]

library_books

Interpreting short tandem repeat variations in humans using mutational constraint

2017
Nat Genet
PMCID: 5679271
PMID: 28892063
DOI: 10.1038/ng.3952

[…] from diverse genetic backgrounds sequenced to 30–50x coverage by the sgdp project. we aligned reads to the hg19 reference genome using bwa-mem and the resulting alignments were used as input to lobstr (methods). high quality snp genotypes were obtained from our previous study. we used these as input to psmc to estimate the local tmrca between haplotypes of each diploid individual. […]


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lobSTR institution(s)
Harvard–MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA; Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel
lobSTR funding source(s)
Supported by the National Defense Science & Engineering Graduate Fellowship, a fellowship from the Edmond Safra Center for Bioinformatics at Tel-Aviv University, Israeli Science Foundation grant ISF 1227/09 and an IBM Open Collaborative Research grant.

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