Herald:The Biostar Herald for Monday, November 01, 2021

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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 Mensur Dlakic, Istvan Albert, GenoMax, and was edited by Istvan Albert,

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we should completely eliminate quality values from sequence archives (SRA, ENA). Huge waste of space, not only in SRA/ENA but also the 1000s of labs that download them https://t.co/iTFa6REe0D

— Steven Salzberg (@StevenSalzberg1) October 23, 2021

submitted by: Istvan Albert

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ColabFold - Making protein folding accessible to all (www.biorxiv.org)

AlphaFold2 and RoseTTAFold for the masses

submitted by: Mensur Dlakic

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DeepConsensus: Gap-Aware Sequence Transformers for Sequence Correction (www.biorxiv.org)

DeepConsensus

submitted by: GenoMax

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Improving long-read consensus sequencing accuracy with deep learning (www.biorxiv.org)

Deep learning to improve long-read consensus PacBio.

submitted by: GenoMax

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GitHub - mskcc/vcf2maf: Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms (github.com)

Though the most useful feature is the extensive support in parsing a wide range of crappy MAF-like or VCF-like formats we've seen out in the wild.

submitted by: Istvan Albert

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A field-wide assessment of differential high throughput sequencing reveals widespread bias (www.biorxiv.org)

Analysis of GEO submission file structures places an overall 56% upper limit to reproducibility without querying other sources. We further show that only 23% of experiments resulted in theoretically expected p value histogram shapes, although both reproducibility and p value distributions show marked improvement over time.

submitted by: Istvan Albert

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