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This edition of the Herald was brought to you by contribution from GenoMax, Istvan Albert, Rob, and was edited by GenoMax, Istvan Albert,
Complex genetic variation in nearly complete human genomes | bioRxiv (www.biorxiv.org)
Complex genetic variation in human genomes.
submitted by: GenoMax
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment | bioRxiv (www.biorxiv.org)
This work describes an approach for single-cell ATAC-seq processing that is fast and lightweight in terms of memory requirements. This pipeline is also within the alevin-fry ecosystem, which allows one to unify the processing single-cell and single-nucleus RNA-seq, single-cell ATAC-seq and many feature barcoding assays within this open-source framework.
submitted by: Rob
GitHub - complextissue/pytximport: Feature-rich Python implementation of the tximport package for gene count estimation. (github.com)
pytximport is a Python package for efficient (gene-)count estimation from transcript quantification files produced by pseudoalignment/quasi-mapping tools such as salmon, kallisto, rsem and others. pytximport is a port of the popular tximport Bioconductor R package.
submitted by: Istvan Albert
GitHub - kcleal/superintervals: Fast interval intersection library (github.com)
A fast, memory-efficient data structure for interval intersection queries. SuperIntervals uses a novel superset-index approach that maintains intervals in position-sorted order, enabling cache-friendly searches and SIMD-optimized counting.
submitted by: Istvan Albert
GitHub - jakobnissen/samstrip: Strip SAM files of data not needed for alignment computations (github.com)
This command-line tool removes data from SAM files which does not contain any information about alignment location or quality.
By default, the SEQ and QUAL fields are emptied, and all auxiliary fields except the NM field is removed. This can often reduce the size of BAM files by 90%.
submitted by: Istvan Albert
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