Herald:The Biostar Herald for Monday, August 28, 2023
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10 months ago
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This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,


We introduce Gonomics, an open-source collection of command line programs and bioinformatic libraries implemented in Go that unites readability and performance for genomic analyses. Gonomics contains packages to read, write, and manipulate a wide array of file formats (e.g. FASTA, FASTQ, BED, BEDPE, SAM, BAM, and VCF), and can convert and interface between these formats.

submitted by: Istvan Albert

submitted by: Istvan Albert

submitted by: Istvan Albert

[2308.07333] Computational reproducibility of Jupyter notebooks from biomedical publications (arxiv.org)

Out of 27271 notebooks from 2660 GitHub repositories associated with 3467 articles [ ...] 1203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones.

submitted by: Istvan Albert

Flexiplex: A versatile demultiplexer and search tool for omics data | bioRxiv (www.biorxiv.org)

We developed Flexiplex, a versatile and fast sequence searching and demultiplexing tool for omics data, which is based on the Levenshtein distance and thus allows imperfect matches. We demonstrate Flexiplex's application on three use cases, identifying cell line specific sequences in Illumina short-read single cell data, and discovering and demultiplexing cellular barcodes from noisy long-read single cell RNA-seq data. We show that Flexiplex achieves an excellent balance of accuracy and computational efficiency compared to leading task-specific tools. Flexiplex is available at https://davidsongroup.github.io/flexiplex/.

submitted by: Istvan Albert

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At the risk of sounding stupid: how can we view the full threads of tweets from these posts, like Steven Salzberg's 1/6 versus his other 5/6? Do we have be logged into twitter these days for that?


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