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, and was edited by Istvan Albert,
Eleven strategies for making reproducible research and open science training the norm at research institutions | eLife (elifesciences.org)
Here, we outline eleven strategies for making training in these practices the norm at research institutions. The strategies, which emerged from a virtual brainstorming event organized in collaboration with the German Reproducibility Network, are concentrated in three areas: (i) adapting research assessment criteria and program requirements; (ii) training; (iii) building communities.
submitted by: Istvan Albert
geNomad (portal.nersc.gov)
geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptome
submitted by: Istvan Albert
https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyad179/7289162
In this project, we focused on characterizing CNVs from high coverage WGS data of over 1,000 individuals from the Northern Sweden Population Health Study (NSPHS) (Höglund et al. 2019). We called CNVs using CNVnator, and tested for association between CNVs and the variation in a large set of proteins (N = 438) that represent well-established or exploratory biomarkers of disease. Subsequently, we resequenced 15 individuals from our cohort using SMRT technology, to verify the CNVs at individual-level.
submitted by: Istvan Albert
GitHub - bcgsc/NanoSim: Nanopore sequence read simulator (github.com)
NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology.
submitted by: Istvan Albert
GitHub - bluenote-1577/sylph: ultrafast ANI querying and taxonomic profiling for metagenomic shotgun samples by abundance-corrected minhash. (github.com)
sylph is a program that can perform ultrafast (1) ANI querying or (2) metagenomic profiling for metagenomic shotgun samples.
submitted by: Istvan Albert
Presenting sylph (https://t.co/WGX3W1yOjT), a fast, precise metagenomic profiler. Work done with @YunWilliamYu.
sylph is highly accurate at the species level and takes ~1 minute and 16 GB RAM to profile against 85k prokaryotes and 2.9 million viral genomes.
1/10 https://t.co/Bsx5tOr0GE pic.twitter.com/SkaRxKTSao
— Jim Shaw (@jim_elevator) November 21, 2023
Presenting sylph (https://t.co/WGX3W1yOjT), a fast, precise metagenomic profiler. Work done with @YunWilliamYu.
sylph is highly accurate at the species level and takes ~1 minute and 16 GB RAM to profile against 85k prokaryotes and 2.9 million viral genomes.
1/10 https://t.co/Bsx5tOr0GE pic.twitter.com/SkaRxKTSao
submitted by: Istvan Albert
GitHub - igvteam/igv-reports: Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files. (github.com)
A Python application to generate self-contained HTML reports that consist of a table of genomic sites or regions and associated IGV views for each site. The generated HTML page contains all data neccessary for IGV as uuencoded blobs. It can be opened within a web browser as a static page, with no depenency on the original input files.
submitted by: Istvan Albert
Comparative Genome Viewer - Home (www.ncbi.nlm.nih.gov)
This tool allows you to compare two genomes based on assembly-assembly alignments provided by NCBI.
submitted by: Istvan Albert
GitHub - matloff/TidyverseSkeptic: An opinionated view of the Tidyverse "dialect" of the R language. (github.com)
The context of this essay is how to teach R to students without prior coding background. These learners typically come from the social sciences, business, or the humanities, sometimes from the life sciences.
I believe that teaching R via the Tidyverse is counterproductive for this group of learners.
submitted by: Istvan Albert
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