asvtab_illPE: Create ASV table from filtered PAIRED-END Illumina reads

In peterolah001/BiMiCo: Biomap Microbiome Core methods

Create ASV table from filtered PAIRED-END Illumina reads

Description

Given a set of PE 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_illPE(filt_out, batch, mtthread = F, mergepairs = F)

Arguments

filt_out	(Required) Path to filtered reads from previous step (dir containing "DADA2_filt_FWD" and DADA2_filt_REV" dirs)
batch	(Required) List indicating the sequencing batch (e.g., a column of phenodata with batch information)
mtthread	(Optional) Boolean, enables multithreading (not recommended in Rstudio) Default=F
mergepairs	(Optional) Boolean, to merge read pairs (recommended) or only concatenate (if there's no overlap between the majority of reads, it is recommended to inspect trimming). Default=F

Examples

asvtab_illPE()

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