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,
Welcome to open-cravat’s documentation! — open-cravat documentation (docs.opencravat.org)
OpenCRAVAT is a python package that performs genomic variant interpretation including variant impact, annotation, and scoring. There is a web-based version of OpenCRAVAT (https://run.opencravat.org) but it can also be installed locally and is easy to integrate into bioinformatics pipelines. OpenCRAVAT has a modular architecture with a wide variety of analysis modules that can be selected and installed/run based on the needs of a given study.
submitted by: Istvan Albert
The complete telomere-to-telomere sequence of a mouse genome (www.science.org)
T2T genome sequence of a cell line for a haploid androgenetic embryonic stem cell line originally derived from the C57BL/6 mouse strain.
submitted by: GenoMax
Recommendations for Bioinformatics in Clinical Practice | bioRxiv (www.biorxiv.org)
This article presents consensus recommendations developed by 13 clinical bioinformatics units taking part in the Nordic Alliance for Clinical Genomics (NACG), by expert bioinformaticians working in clinical production.
Key recommendations include adopting the hg38 genome build as the reference and a standard set of recommended analyses, including the use of multiple tools for structural variant (SV) calling and in-house data sets for filtering recurrent calls.
submitted by: Istvan Albert
iSeq: an integrated tool to fetch public sequencing data (academic.oup.com)
TLDR: iSeq: an easy-to-run bash script that requires that you have conda installed then it will run fasterq-dump for you
The staggering advances of modern bioinformatics!
submitted by: Istvan Albert
A BLAST from the past: revisiting blastp's E-value (academic.oup.com)
Here we critically evaluate the E-values provided by the standard protein BLAST (blastp), showing that they can be at times significantly conservative while at others too liberal. We offer an alternative approach based on generating a small sample from the null distribution of random optimal alignments, and testing whether the observed alignment score is consistent with it.
submitted by: Istvan Albert
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