read_sequences_from_fastq {minSNPs}

read_sequences_from_fastq

Description

read_sequences_from_fastq get the sequences from a fastq file, it completely ignores the quality scores

Usage

read_sequences_from_fastq(
  fastq_file,
  force_to_upper = TRUE,
  skip_n_reads = 0,
  max_n_reads = -1,
  output_quality = TRUE,
  quality_offset = 33,
  bp = MulticoreParam()
)

Arguments

fastq_file

location of the fastq file

force_to_upper

whether to transform sequences to upper case, default to TRUE

skip_n_reads

number of reads to skip, default to 0

max_n_reads

maximum number of reads to read, default to -1 (all)

output_quality

whether to output the quality scores, default to TRUE

quality_offset

the quality offset to use, default to 33

bp

BiocParallel backend to use for parallelization

Value

will return a list of sequences, with qualities as attribute