fastq_pair: FASTQ PAIR

In blit: Bioinformatics Library for Integrated Tools

FASTQ PAIR

Description

Rewrite paired end fastq files to make sure that all reads have a mate and to separate out singletons.

Usually when you get paired end read files you have two files with a /1 sequence in one and a /2 sequence in the other (or a /f and /r or just two reads with the same ID). However, often when working with files from a third party source (e.g. the SRA) there are different numbers of reads in each file (because some reads fail QC). Spades, bowtie2 and other tools break because they demand paired end files have the same number of reads.

Usage

fastq_pair(
  fq1,
  fq2,
  ...,
  hash_table_size = NULL,
  max_hash_table_size = NULL,
  fastq_pair = NULL
)

fastq_read_pair(fastq_files)

Arguments

fq1, fq2	A string of fastq file path.
...	<dynamic dots> Additional arguments passed to fastq_pair command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using shQuote(). Details see: cmd_help(fastq_pair()).
hash_table_size	Size of hash table to use.
max_hash_table_size	Maximal hash table size to use.
fastq_pair	A string of path to fastq_pair command.
fastq_files	A character of the fastq file paths.

Value

A command object.

See Also

• https://github.com/linsalrob/fastq-pair

• cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_conda()

• cmd_on_start()/cmd_on_exit()

• cmd_on_succeed()/cmd_on_fail()

• cmd_parallel()

Other commands: allele_counter(), cellranger(), conda(), gistic2(), kraken2(), kraken_tools(), perl(), pyscenic(), python(), samtools(), seqkit(), trust4()

blit documentation built on April 12, 2025, 1:16 a.m.