lobSTR

[…] 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 […]

[…] 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- () […]

[…] 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, […]

[…] 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 […]

[…] 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 […]

[…] 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. […]