Herald:The Biostar Herald for Tuesday, June 28, 2022
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Biostar 960

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, and was edited by Istvan Albert,


CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes | bioRxiv (www.biorxiv.org)

submitted by: Mensur Dlakic


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

Here we use simulated benchmarking data that reflects many properties of real data, including polymorphisms, intron signal and non-uniform coverage, allowing for systematic comparative analyses of isoform quantification accuracy and its impact on differential expression analysis. Genome, transcriptome and pseudo alignment-based methods are included; and a simple approach is included as a baseline control.

submitted by: Istvan Albert


From Easy to Hopeless - Predicting the Difficulty of Phylogenetic Analyses | bioRxiv (www.biorxiv.org)

How likely is phylogenetic tree convergence? https://github.com/tschuelia/PyPythia

submitted by: Mensur Dlakic


GitHub - broadinstitute/gtex-pipeline: GTEx & TOPMed data production and analysis pipelines (github.com)

Analysis pipelines for the GTEx Consortium and TOPMed

The repository contains analysis pipelines for:

  • RNA-seq alignment, quantification, and quality control
  • eQTL mapping and annotation
  • Allele-specific expression quantification
  • Generation of the collapsed annotation used for gene-level expression quantification

submitted by: Istvan Albert


Jvarkit : Java utilities for Bioinformatics (lindenb.github.io)

Jvarkit : Java utilities for Bioinformatics

A huge suite of utilities solving peculiar yet essential corner cases that spice up every bioinformatician's life.

submitted by: Istvan Albert


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