Herald:The Biostar Herald for Monday, May 30, 2022
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29 days ago
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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 Laura, Istvan Albert, and was edited by Istvan Albert,


Tweet thread on gget's versatility with examples showcasing how it can efficiently solve database querying tasks in genomic data analysis.

submitted by: Laura


'gget' enables efficient querying of genomic databases, such as Ensembl, UniProt, NCBI, and Enrichr, directly into a Python or command-line programming environment. It was designed to support genomic data analysis.

submitted by: Laura

GitHub - lskatz/Kalamari: A curated database of completed assemblies with taxonomy IDs (github.com)

Kalamari is a database of completed and public assemblies, backed by trusted institutions. These assemblies can be further used in formatted databases such as Kraken or Blast.

submitted by: Istvan Albert

Beyond grep: ack v3.5.0 (beyondgrep.com)

ack is more usable version of grep (finds patterns inside files). One of the first tools I install on a new system. Makes you more productive.


See also fd a better file finder:

submitted by: Istvan Albert

submitted by: Istvan Albert

GitHub - metagenome-atlas/atlas: ATLAS - Three commands to start analyzing your metagenome data (github.com)

Metagenome-atlas is a metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.

submitted by: Istvan Albert

PhD students face cash crisis with wages that don’t cover living costs (www.nature.com)

Salaries for PhD students in the biological sciences fall well below the basic cost of living at almost every institution and department in the United States, according to data collected by two PhD students.

submitted by: Istvan Albert

A survey of mapping algorithms in the long-reads era | bioRxiv (www.biorxiv.org)

In this survey article, we provide an overview of existing mapping methods for long reads with insights into algorithmic details

submitted by: Istvan Albert

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