LobSTR
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Application data |
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| Created by | Melissa Gymrek |
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| Biological application domain(s) | Sequencing |
| Principal bioinformatics method(s) | Repeat sequence organisation analysis |
| Technology | Illumina |
| Created at | Whitehead Institute for Biomedical Research |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTQ, BAM |
| Output format(s) | BAM, Custom |
| Software features | Fast, Scalable, sequence alignment, Gapped alignment |
| Programming language(s) | C++, R, Python |
| Software libraries | FFTW, Boost, BamTools, Zlib, Biopython |
| Licence | Freeware |
| Operating system(s) | UNIX |
| Contact: | yaniv@wi.mit.edu |
Summary: lobSTR is an alignment and genotyping tool for profiling short tandem repeats from next generation sequencing data
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Description
lobSTR is an algorithm for profiling short tandem repeats (STRs) from whole genome sequencing datasets. STRs provide an enormous source of genetic variation between individuals, with one human genome harboring tens of thousands of STR polymorphisms. Until now, STR genotyping has been limited in sequencing studies due to the unique gapped alignment problem they present. lobSTR is a novel algorithm that meets these challenges to rapidly and accurately profile hundreds of thousands of genome-wide STRs. lobSTR accepts raw reads in FASTQ/FASTA or BAM format and provides the user with the genotyping results.
Links
References
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| Web Search | Wiki Sites | Scientific |
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