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 ATpoint, Istvan Albert, lieven.sterck,
RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis | BMC Bioinformatics | Full Text (bmcbioinformatics.biomedcentral.com)
RNAdetector is a new software that aims to fill an essential gap between the needs of biomedical and research labs to process RNA-Seq data and their common lack of technical background in performing such analysis, which usually relies on outsourcing such steps to third party bioinformatics facilities or using expensive commercial software.
submitted by: natay.aberra
A cartoon guide to bioinformatics by a novice coder (www.nature.com)
Ed Himelblau was a cartoonist before he learnt to write code. Now, the geneticist hopes his drawings will help others who embrace bioinformatics later in their careers.
submitted by: Istvan Albert
GitHub - danielecook/Awesome-Bioinformatics: A curated list of awesome Bioinformatics libraries and software. (github.com)
A curated list of awesome Bioinformatics software, resources, and libraries. Mostly command line based, and free or open-source.
submitted by: natay.aberra
The complete sequence of a human genome | bioRxiv (www.biorxiv.org)
21 years after annonoucning the completion of the human genome project we may be "closing in" (pun intended) on actually finishing the human genome.
The new T2T-CHM13 reference includes gapless assemblies for all 22 autosomes plus Chromosome X, corrects numerous errors, and introduces nearly 200 million bp of novel sequence containing 2,226 paralogous gene copies, 115 of which are predicted to be protein coding. The newly completed regions include all centromeric satellite arrays and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies for the first time.
submitted by: Istvan Albert
GitHub - chanzuckerberg/shasta: De novo assembly from Oxford Nanopore reads. (github.com)
The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.
While I have not evaluated the tool myself, the presentation and documentation of it appear to be outstanding.
submitted by: Istvan Albert
GitHub - mdshw5/simplesam: Simple pure Python SAM parser and objects for working with SAM records (github.com)
Simplesam is a pure Python SAM file reader that is easier to install than pysam and offers a more straightforward and more logical programming interface.
submitted by: Istvan Albert
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