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lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data.
Features
- (v2.0.0) Support for paired end reads. lobSTR uses mate pair information to increase confidence in STR alignments. lobSTR can still run in single-end mode.nment quality and produces accurate CIGAR scores that can be used for downstream SNP calling and viewing on samtools tview.
- (v2.0.0) Paired-end read stitching: when possible, lobSTR will stitch overlapping paired-end reads that in some cases can span longer STRs than possible with a single read.
- (v2.0.0) Support for reading gzipped FASTA and FASTQ files.
- (v.2.0.0) Alignment of partially spanning reads: lobSTR reports alignments of reads that only partially span STR regions. The allele length reported gives a lower bound on the true STR allele.
- (v2.0.0) Conversion of allelotype output to VCF format
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Great stuff.
