Herald:The Biostar Herald for Wednesday, June 02, 2021

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[Biostar]

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, natay.aberra, and was edited by Istvan Albert, Ram, Carlo Yague,

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3 days 3 different time zones and that's the Bioinformatics Education Summit done for another year #BES2021.

Today we covered effective and efficient building of infrastructure and activities in Low and middle income countries (LMICS).

A huge thank you to everyone involved. pic.twitter.com/oBpYVAt2DK

— EMBL-EBI Training (@EBItraining) May 26, 2021

submitted by: natay.aberra

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GitHub - tjiangHIT/cuteSV: Long read based human genomic structural variation detection with cuteSV (github.com)

A long-read-based human genomic structural variation detection with an evidently cute name. That's a bioinformatics tool name that we can rally around.

submitted by: Istvan Albert

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Crac: Funny And/Or Weird Names For Bioinformatics Tools (www.biostars.org)

Since we were talking about names .... here is an oldie on the topic

submitted by: Istvan Albert

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For the 60th episode of the #bioinformatics chat, we're excited to bring you a conversation with @mikelove about his classic package DESeq2https://t.co/sJtesy8Xsg

— the bioinformatics chat (@bioinfochat) May 12, 2021

submitted by: Istvan Albert

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Comparative evaluation of full-length isoform quantification from RNA-Seq | BMC Bioinformatics | Full Text (bmcbioinformatics.biomedcentral.com)

A massive paper that compares a whole slew of isoform quantification (not alignment) tools.

How good are your gene expression count tables? You know, the data that is then used to produce differential expressions.

"Here we present a benchmarking analysis of the six most popular isoform quantification methods: kallisto, Salmon, RSEM, Cufflinks, HTSeq, and featureCounts, based on a survey of the literature"

submitted by: Istvan Albert

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Vcflib and tools for processing the VCF variant call format | bioRxiv (www.biorxiv.org)

Dealing with VCF files is a ubiquitous need for bioinformaticians. The VCFlib is project states that

Here we present over 125 useful and much used free and open-source software tools and libraries, part of vcflib tools and bio-vcf.

now, unfortunately, this also means that your filesystem will be littered with programs prefixed with vcf such as:

vcfcreatemulti                vcfmultiway                   vcfsort
vcfdistance                   vcfmultiwayscripts            vcfstats
vcfecho                       vcfnobiallelicsnps            vcfstreamsort
vcfentropy                    vcfnoindels                   vcfuniq

but then we kind of have learned to deal with that, haven't we...

On the bright side if you need to massage VCF files into the right format make sure to check out the project

submitted by: Istvan Albert

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Minimap2 v2.19 released with better and more contiguous alignment over long INDELs and in highly repetitive regions, improvements backported from unimap. These represent the most significant algorithmic change since v2.1. Use with caution. https://t.co/YiZU0QsUsm

— Heng Li (@lh3lh3) May 27, 2021

The mapping God keeps on providing us with better tools. Hallelujah!

submitted by: Istvan Albert

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A hypothesis is a liability | Genome Biology | Full Text (genomebiology.biomedcentral.com)

An interesting back and forth, make sure to read the correspondence on data and hypothesis.

Smart people on both sides on an issue that is just as divisive as political polarization. Should you have a hypothesis?

submitted by: Istvan Albert

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Answer 1

[Istvan Albert]

This is the inaugural Biostar Herald, a way to share short, relevant bioinformatics tidbits that do not warrant an entire post.

We invite all users to submit interesting content at the Herald link on the top bar, also accessible here:

https://www.biostars.org/herald/

You may also receive the Herald in an email, click toggle subscription above.

Moderators will review the various submissions, and accept/decline links. Accepted links will be published periodically in a digest form, once a week perhaps.

We will keep working on formatting and other issues.