Herald:The Biostar Herald for Thursday, July 07, 2022
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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 GenoMax, Istvan Albert, and was edited by Istvan Albert,

ScienceDirect (www.sciencedirect.com)

Advances in long-read DNA sequencing technologies have enabled researchers to obtain high-quality genomes and finely resolve structural variants (SVs) in many species, even from small laboratories. The hands-on protocol presented here will guide you through the process of analyzing three different types of publicly available Drosophila melanogaster datasets obtained using current long-read sequencing technologies. We hope that this protocol will help in guiding researchers who are new to the process of long-read sequencing analysis.

submitted by: Istvan Albert

submitted by: Istvan Albert

Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing | Nature Methods (www.nature.com)

Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.

submitted by: Istvan Albert

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes | Genome Biology | Full Text (genomebiology.biomedcentral.com)

There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 samples from three bacterial species and an outbreak of 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate on a large (N=13k) M. tuberculosis cohort, building a map of non-synonymous SNPs and indels in a region where all such variants are assumed to cause rifampicin resistance.

submitted by: Istvan Albert

GitHub - edgardomortiz/vcf2phylip: Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis (github.com)

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

submitted by: Istvan Albert

High-throughput total RNA sequencing in single cells using VASA-seq | Nature Biotechnology (www.nature.com)

Improved method for total RNAseq from single cells.

submitted by: GenoMax

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