Tutorials — Mash 2.0 documentation - Read the Docs
WEBIf a read set potentially has multiple genomes, it can be “screened” against the database to estimate how well each genome is contained in the read set. We can use the SRA Toolkit to download ERR024951: fastq-dump ERR024951. …and screen it against Refseq Genomes (link above), sorting the results:
Mash Screen: what's in my sequencing run? - GitHub Pages
WEBWhen calling screen against a protein database, Mash will automatically perform six-frame translation on the input nucleotide sequences. This could be handy for quickly computing containment of viruses or individual genes within metagenomes.
Mash Screen: high-throughput sequence containment estimation …
WEBNov 5, 2019 · Mash Screen is designed to efficiently estimate the containment of whole genomes or proteomes and can also be used to detect the presence of any set of related sequences (e.g., plasmids, functional pathways).
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Mash Screen: high-throughput sequence containment estimation …
WEBMash Screen: high-throughput sequence containment estimation for genome discovery. Author (s) Ondov, Brian D.; Starrett, Gabriel J.; Sappington, Anna; Kostic, Aleksandra; Koren, Sergey; ... Show more. Download 13059_2019_Article_1841.pdf (1.492Mb) Publisher with Creative Commons License. Terms of use.
WEBMash Screen: High-throughput sequence containment estimation for genome discovery. Brian D Ondov1,2*, Gabriel J Starrett3, Anna Sappington4, Aleksandra Kostic5, Sergey Koren1, Christopher B Buck3and Adam M Phillippy1. *Correspondence: brian.ondov@nih.gov.
Mash Screen: High-throughput sequence containment estimation …
WEBMar 1, 2019 · Here we describe an online algorithm capable of measuring the containment of genomes and proteomes within either assembled or unassembled sequencing read sets. We describe several use cases, including contamination screening and retrospective analysis of metagenomes for novel genome discovery.
(PDF) Mash Screen: high-throughput sequence containment …
WEBNov 5, 2019 · The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a...