iterativeAssemble: iterativeAssemble

In chutter/MitoCap: Package For extracting, assembling, annotating and aligning mitochondrial genomes from high-throughput sequencing data

iterativeAssemble

Description

Function for removing adaptor sequences from raw Illumina sequence data using the program fastp

Usage

iterativeAssemble(
  input.reads = NULL,
  reference = NULL,
  output.name = NULL,
  mapper = "bbmap",
  min.iterations = 5,
  max.iterations = 20,
  min.length = 16000,
  max.length = 30000,
  min.ref.id = 0.75,
  memory = 1,
  threads = 1,
  spades.path = "spades.py",
  bbmap.path = "bbmap.sh",
  cap3.path = "cap3",
  resume = TRUE,
  overwrite = FALSE,
  quiet = TRUE
)

Arguments

input.reads	path to a folder of raw reads in fastq format.
reference	a csv file with a "File" and "Sample" columns, where "File" is the file name and "Sample" is the desired renamed file
output.name	the new directory to save the adaptor trimmed sequences
mapper	"Sample" to run on a single sample or "Directory" to run on a directory of samples
min.iterations	system path to fastp in case it can't be found
max.iterations	system path to fastp in case it can't be found
min.length	system path to fastp in case it can't be found
max.length	system path to fastp in case it can't be found
min.ref.id	system path to fastp in case it can't be found
threads	number of computation processing threads
spades.path	system path to fastp in case it can't be found
bbmap.path	system path to fastp in case it can't be found
cap3.path	system path to fastp in case it can't be found
resume	TRUE to skip samples already completed
overwrite	TRUE to overwrite a folder of samples with output.dir
quiet	TRUE to supress screen output
mem	amount of system memory to use

Value

a new directory of adaptor trimmed reads and a summary of the trimming in logs/

Examples

your.tree = ape::read.tree(file = "file-path-to-tree.tre")
astral.data = astralPlane(astral.tree = your.tree,
                          outgroups = c("species_one", "species_two"),
                          tip.length = 1)

chutter/MitoCap documentation built on July 17, 2025, 12:04 a.m.