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 zx8754, Mensur Dlakic, Istvan Albert, and was edited by Istvan Albert,
GitHub - hsinnan75/GSAlign: GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison (github.com)
GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
TLDR: produces pairwise alignments, with either MAF or VCF output pretty darn quick
Aligns 50 million bp genomes in about 40 seconds.
submitted by: Istvan Albert
Contrastive learning on protein embeddings enlightens midnight zone | bioRxiv (doi.org)
Detecting distant homology from protein language models.
submitted by: Mensur Dlakic
[2203.14309] DeepDPM: Deep Clustering With an Unknown Number of Clusters (arxiv.org)
https://github.com/BGU-CS-VIL/DeepDPM
submitted by: Mensur Dlakic
Experienced Bioinformaticians:
Comment below the one thing you'd like to tell junior Bioinformaticians.
New Bioinformaticians:
Read below for an awesome list of career tips.
— Nils Homer (@nilshomer) April 6, 2022
Experienced Bioinformaticians:
Comment below the one thing you'd like to tell junior Bioinformaticians.
New Bioinformaticians:
Read below for an awesome list of career tips.
submitted by: Istvan Albert
GitHub - rrwick/Filtlong: quality filtering tool for long reads (github.com)
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
submitted by: Istvan Albert
awesome-genome-visualization (cmdcolin.github.io)
awesome-genome-visualization A list of interesting genome visualizers, genome browsers, or genome-browser-like implementations https://github.com/cmdcolin/awesome-genome-visualization
submitted by: zx8754
De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing. | bioRxiv (www.biorxiv.org)
De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing.
submitted by: Istvan Albert
Prime-seq, efficient and powerful bulk RNA sequencing | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it performs equivalently to TruSeq, a standard bulk RNA-seq method, but is fourfold more cost-efficient due to almost 50-fold cheaper library costs
submitted by: Istvan Albert
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