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 GenoMax, Istvan Albert, and was edited by Istvan Albert,
x.com (x.com)
I just tagged new releases for seqkit https://github.com/shenwei356/seqkit/releases/tag/v2.9.0, taxonkit https://github.com/shenwei356/taxonkit/releases/tag/v0.18.0, csvtk https://github.com/shenwei356/csvtk/releases/tag/v0.31.0
There are a lot of changes, please have a look.
submitted by: Istvan Albert
GitHub - google/deeppolisher: Transformer-based sequence correction method for genome assembly polishing (github.com)
DeepPolisher is a transformer-based sequencing correction method similar to DeepConsensus. DeepPolisher is designed to identify errors in genome assemblies. DeepPolisher takes haplotype-specific reads aligned to phased assemblies and produces a VCF file containing potential errors in the assembly. Currently, DeepPolisher can take PacBio HiFi-based assemblies and read alignments to identify potential errors.
submitted by: Istvan Albert
AllTheBacteria documentation — AllTheBacteria documentation (allthebacteria.readthedocs.io)
In this study we describe the initial v0.1 data release of 1,932,812 assemblies (combining 1,271,428 new assemblies with the 661k dataset). All 1.9 million have been uniformly re-processed for quality criteria and to give taxonomic abundance estimates with respect to the GTDB phylogeny. Using an evolution-informed compression approach, the full set of genomes is just 102Gb in batched xz archives. We also provide multiple search indexes. Finally, we outline plans for future annotations to be provided in further releases.
submitted by: Istvan Albert
A near telomere-to-telomere phased reference assembly for the male mountain gorilla | bioRxiv (www.biorxiv.org)
The endangered mountain gorilla, Gorilla beringei beringei, faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for a male mountain gorilla generated using PacBio HiFi (26.77X ave. coverage) and Oxford Nanopore Technologies (52.87X ave. coverage) data.
submitted by: Istvan Albert
x.com (twitter.com)
Great pleasure to work with shenwei356 on a new indexing and alignment scheme, called LexicMap: https://biorxiv.org/content/10.1101/2024.08.30.610459v1 We have been working on uniformly reassembling, QC-ing and annotating all bacterial (+ now archaeal) data, & wanted to be able to do full alignment to it....
submitted by: Istvan Albert
A single-molecule nanopore sequencing platform | bioRxiv (www.biorxiv.org)
A nanopore sequencing platform from BGI/MGI.
submitted by: GenoMax
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