lobSTR protocols

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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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Documentation


Maintainer


  • person_outline Yaniv Erlich <>

Additional information


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

Publication for lobSTR

lobSTR in pipelines

 (3)
2017
PMCID: 5333174
PMID: 28251872
DOI: 10.1186/s12862-016-0870-2

[…] we kept snp positions near indels, except for the regions with high probability of containing strs (for this, we measured the “dimeric” entropy value calculated in a the way close to that of lobstr []). rules in the general form (those operating with variables such as ‘read count’ or ‘base/mapping quality’) were always preferred over hard-coded exclusion of a particular position […]

2017
PMCID: 5443785
PMID: 28539617
DOI: 10.1038/s41598-017-02600-8

[…] sra toolkits, which were aligned to the pig reference genome via bowtie 2 with default settings. the resulting bam files were sorted with samtools, and then used for ssr profiling with the program lobstr. for each ssr locus, the average coverage was calculated as the number of total mapped reads divided by the number of samples with available genotypes., after primary genotyping with lobstr, […]

2016
PMCID: 5381564
PMID: 28172841
DOI: 10.1093/gbe/evw256

[…] explore the contributions of strs involved in gene function, we overlapped the strs with exon regions of refseq genes. we found 204 strs were embedded in exon regions of 194 genes., to confirm lobstr prediction, we randomly selected 18 strs of different motif sizes (including di-, tri-, and tetranucleotides) and used sanger sequencing to confirm whether the correct genotypes were derived […]


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lobSTR in publications

 (34)
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 […]

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- () […]

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, […]

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 […]

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 […]


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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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