asvtab_illSE: Create ASV table from filtered SINGLE-END Illumina reads

In peterolah001/BiMiCo: Biomap Microbiome Core methods

Create ASV table from filtered SINGLE-END Illumina reads

Description

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

Usage

asvtab_illSE(readfiles, batch, n = 1e+06, mtthread = F)

Arguments

readfiles	(Required) Path to SE Illumina quality-filtered fastq DIRECTORY (e.g. filt_fqs_dir in tutorial)
batch	(Required) List indicating the sequencing batch (e.g., a column of phenodata with batch information)
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

Examples

asvtab_illSE()

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