Herald:The Biostar Herald for Wednesday, June 02, 2021
Entering edit mode
6 months ago
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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 Istvan Albert, natay.aberra, and was edited by Istvan Albert, Ram, Carlo Yague,

submitted by: natay.aberra

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

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

submitted by: Istvan Albert

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

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

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

submitted by: Istvan Albert

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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herald • 519 views
Entering edit mode
6 months ago

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:


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

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