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This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,
GitHub - shenwei356/kmcp: Accurate metagenomic profiling && Fast large-scale sequence/genome searching (github.com)
KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
submitted by: Istvan Albert
GitHub - marbl/CHM13: The complete sequence of a human genome (github.com)
We have sequenced the CHM13hTERT human cell line with a number of technologies. Human genomic DNA was extracted from the cultured cell line. As the DNA is native, modified bases will be preserved. The data includes 30x PacBio HiFi, 120x coverage of Oxford Nanopore, 70x PacBio CLR, 50x 10X Genomics, as well as BioNano DLS and Arima Genomics HiC. Most raw data is available from this site, with the exception of the PacBio data which was generated by the University of Washington/PacBio and is available from NCBI SRA.
submitted by: Istvan Albert
GitHub - broadinstitute/gtex-pipeline: GTEx & TOPMed data production and analysis pipelines (github.com)
This repository contains analysis pipelines for:
- RNA-seq alignment, quantification, and quality control
- eQTL mapping and annotation
- Allele-specific expression quantification
- Generation of the collapsed annotation used for gene-level expression quantification
submitted by: Istvan Albert
Contamination detection in genomic data: more is not enough | Genome Biology | Full Text (genomebiology.biomedcentral.com)
The decreasing cost of sequencing and concomitant augmentation of publicly available genomes have created an acute need for automated software to assess genomic contamination. During the last 6 years, 18 programs have been published, each with its own strengths and weaknesses. Deciding which tools to use becomes more and more difficult without an understanding of the underlying algorithms. We review these programs, benchmarking six of them, and present their main operating principles.
submitted by: Istvan Albert
viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data | Genome Biology | Full Text (genomebiology.biomedcentral.com)
We describe the viralFlye tool for identification and analysis of metagenome-assembled viruses in long-read assemblies. We show it significantly improves viral assemblies and demonstrate that long-reads result in a much larger array of predicted virus-host associations as compared to short-read assemblies. We demonstrate that the identification of novel CRISPR arrays in bacterial genomes from a newly assembled metagenomic sample provides information for predicting novel hosts for novel viruses.
submitted by: Istvan Albert
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