Herald:The Biostar Herald for Tuesday, February 28, 2023
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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 GenoMax, Istvan Albert, and was edited 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


Megadepth: efficient coverage quantification for BigWigs and BAMs - PubMed (pubmed.ncbi.nlm.nih.gov)

Megadepth is a fast tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files, using substantially less memory than the next-fastest competitor. Megadepth can summarize coverage within all disjoint intervals of the Gencode V35 gene annotation for more than 19 000 GTExV8 BigWig files in approximately 1 h using 32 threads. Megadepth is available both as a command-line tool and as an R/Bioconductor package providing much faster quantification compared to the rtracklayer package.

submitted by: Istvan Albert


Releases · COMBINE-lab/salmon · GitHub (github.com)

Salmon 1.10 released.

submitted by: GenoMax


submitted by: Istvan Albert


Release 1.17 · samtools/samtools · GitHub (github.com)

Samtools 1.7 released

Improve samtools consensus for platforms with instrument specific profiles, considerably helping for data with very different indel error models and providing base quality recalibration tables

New samtools reset subcommand. Removes alignment information. Alignment location, CIGAR, mate mapping and flags are updated. If the alignment was in reverse direction, sequence and its quality values are reversed and complemented and the reverse flag is reset. Supplementary and secondary alignment data are discarded.

submitted by: Istvan Albert


FixItFelix: improving genomic analysis by fixing reference errors | Genome Biology | Full Text (genomebiology.biomedcentral.com)

The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including 12 with medical relevance. Here, we present FixItFelix, an efficient remapping approach, together with a modified version of the GRCh38 reference genome that improves the subsequent analysis across these genes within minutes for an existing alignment file while maintaining the same coordinates.

submitted by: Istvan Albert


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