waxsys.stat.sra: waxsys.stat.sra

In ababaian/palmid: Viral RNA Dependent RNA Polymerase Analysis Suite

waxsys.stat.sra

Description

Waxsystermes Virus example data. NCBI-STAT is a taxonomic a min-hash / kmer based classification of all the reads in the Sequence Read Archive to known organismal genomes and RefSeq viruses. The summary statistics are available on AWS Athena/Google BigQuery. For all of the SRA, kmer classifications at the taxonomic rank of "Orders" was extracted and is available on the Serratus SQL server. This allows for computational host-inference based on the constellation of organisms associated with a virus across several sequencing libraries.

Usage

data(waxsys.stat.sra)

Format

data.frame with 5320 obs. of 6 variables

Details

#'

• run_id. Sequencing library identifier in the SRA

• order_name. Taxonomic Order (rank) to which kmers are assigned

• tax_label. palmID plotting label for given order

• kmer. Count of the number of kmers matching given order

• kmer_perc. Percent of all kmers for this run_id matching order

• pident. From get.palmSRA(), aa-percent identity of virus-match to input-virus

Source

STAT: Katz et al., 2021

ababaian/palmid documentation built on July 1, 2023, 1:09 a.m.