asvtab_454: Create ASV table from filtered 454 reads

In peterolah001/BiMiCo: Biomap Microbiome Core methods

Create ASV table from filtered 454 reads

Description

Given a set of 454 sequencing reads pre-filtered by the 'prep_454' function, internally generates read error models and outputs chimera-filtered ASV table. ASV table contains ASVs in rows and samples in columns.

Usage

asvtab_454(readfiles, n, mtthread = F, pattern = "_filt.fastq.gz",
  extname = "_filt.fastq.gz")

Arguments

readfiles	(Required) Path to 454 quality-filtered fastq files
n	(Optional) The maximum number of reads to dereplicate at any one time. Controls peak memory requirement. Default=1e6
mtthread	(Optional) Boolean, enables multithreading (not recommended in Rstudio) (default=F)
pattern	(Optional) Pattern (e.g., extension) in input fastq filename, only files with this pattern will be read (default="_filt.fastq.gz")
extname	(Optional) Suffix of input files. (default="_filt.fastq.gz")

Examples

asvtab_454()

peterolah001/BiMiCo documentation built on April 24, 2023, 3:35 a.m.