I haven't done any whole-genome STR analysis from NGS data myself, but are aware of others that have used lobSTR for this. There's also a recent paper [here] that compares a few different STR analysis packages (i.e. RepeatSeq, LobSTR, HipSTR, GangSTR). Here's the concluding paragraph:
In conclusion, all these tools are built to genotype STRs but
have different strengths and weaknesses. Based on our analysis there is
no clear overall winner. RepeatSeq and HipSTR are the best when
considering genotyping error rate even with low coverage. On the other
hand, GangSTR has an advantage because it is the only tool among them
that can call alleles longer than the read length but shows higher error
rate unless looking at only the enclosed class of reads, which in turn
would lose the GangSTR's advantage of picking up long genotypes. In
addition, GangSTR is the newest tool and so comes with reference files for
different reference builds that are periodically updated according to
the tool's webpage. The correct choice of a tool and the
subsequent filtering depends on the aim of the analysis, and might be
influenced by available hardware resources and time limit for running
tools.
In other words, without more information about the specific problem you're trying to solve, it's not clear what the best tool to use is (this is a common issue with Bioinformatics problems).
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創建於2020-07-02T02:55:14Z2020-07-02T02:55:14Z gringer
