Herald:The Biostar Herald for Tuesday, September 14, 2021
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Biostar 240

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here.

This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,


https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab540/6327681

We show that uLTRA produces higher accuracy over state-of-the-art aligners with substantially higher accuracy for small exons on simulated and synthetic data. On simulated data, uLTRA achieves an accuracy of about 60% for exons of length 10 nucleotides or smaller and close to 90% accuracy for exons of length between 11 and 20 nucleotides. On biological data where true read location is unknown, we show several examples where uLTRA aligns to known and novel isoforms containing small exons that are not detected with other aligners. While uLTRA obtains its accuracy using annotations, it can also be used as a wrapper around minimap2 to align reads outside annotated regions.

submitted by: Istvan Albert


[2108.03515] New strategies to improve minimap2 alignment accuracy (arxiv.org)

We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions up to 100kb by default, addressing major weakness in minimap2 v2.18 or earlier.

submitted by: Istvan Albert


Looking Through DeepVariantā€™s Eyes | DeepVariant Blog (google.github.io)

Learn how machine learning works when applied to variation callers.

TLDR: it classifies pileup images, similarity to how visual inspection in IGV works

submitted by: Istvan Albert


Try to beat the DeepVariant by evaluating images

submitted by: Istvan Albert


submitted by: Istvan Albert


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