bbdemux: Demultiplex fusion primers using BBmap Seal

In alexpiper/seqateurs: Tools for trimming and processing sequence data

Demultiplex fusion primers using BBmap Seal

Description

Demultiplex fusion primers using BBmap Seal

Usage

bbdemux(
  install = NULL,
  fwd,
  rev = NULL,
  Fbarcodes = NULL,
  Rbarcodes = NULL,
  restrictleft = NULL,
  out.dir = "demux",
  kmer = NULL,
  hdist = 0,
  degenerate = TRUE,
  force = TRUE,
  threads = NULL,
  mem = NULL,
  interleaved = FALSE
)

Arguments

install	(Required) Install location for bbmap
fwd	(Required) Vector of locations of forward reads
rev	(Optional) Vector of locations of reverse reads
Fbarcodes	(Required) Barcodes used in forward reads
Rbarcodes	(Optional) Barcodes used in reverse reads
restrictleft	(Optional) Defaults to the size of the largest primer. Restricts the kmer search for primer sequences to just the left side of the molecule.
out.dir	(Optional) Default "demux" The path to write the output reads.
kmer	(Optional) default the size of the smallest primer will be used. The kmer size to use for primer searching.
hdist	(Optional) Default = 0. The hamming distance (number of substitution errors) allowed for mismatch to the query primer.
degenerate	(Optional) Default TRUE. Option to search for all possible primer combinations for degenerate primers
force	(Optional) Default TRUE Option to overwrite existing output files.
threads	(Optional) Default autodetect Number of CPU threads to use WARNING: Thread detection can fail on cluster computing currently
mem	(Optional) Default autodetect GB of memory to use WARNING: mem detection can fail on cluster computing currently
interleaved	(Optional) Default FALSE Option to input interleaved reads

Examples

#' \dontrun{
path <- "run_test/"
demuxpath <- file.path(path, "demux") # Filtered forward files go into the path/filtered/ subdirectory

fastqFs <- sort(list.files(path, pattern="R1_001.*", full.names = TRUE))
fastqRs <- sort(list.files(path, pattern="R2_001.*", full.names = TRUE))

bbdemux(install="bin/bbmap", fwd=fastqFs, rev=fastqRs,Fbarcodes = c("GAGGDACW","TGTGGDAC","AGAAGGDAC"),
              Rbarcodes = c("ACGTRATW","TCCGTRAT","CTGCGTRA"),
              degenerate=TRUE, out.dir=demuxpath, threads=1, mem=4,
              hdist=0, force=TRUE)
              }

alexpiper/seqateurs documentation built on July 9, 2023, 7:21 a.m.