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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 DeepVariant’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
Give it a try with the "can you beat DeepVariant?" colab: https://t.co/mNdQYROvrF
— Mark DePristo (@MarkDePristo) September 13, 2021
Give it a try with the "can you beat DeepVariant?" colab: https://t.co/mNdQYROvrF
— Mark DePristo (@MarkDePristo) September 13, 2021Try to beat the DeepVariant by evaluating images
submitted by: Istvan Albert
We discussed this pair of papers in class today. There is a lot to learn from them. pic.twitter.com/UvvEA1kcYj
— Nikolai Slavov (@slavov_n) September 10, 2021
We discussed this pair of papers in class today. There is a lot to learn from them. pic.twitter.com/UvvEA1kcYj
— Nikolai Slavov (@slavov_n) September 10, 2021submitted by: Istvan Albert
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