command line to execute for each of the input file. This command should generate FASTA or FASTQ text and send it to stdout For example: zcat - to uncompress .gz files, bzcat - to uncompress .bz2 files, etc.

paths to files that contain input read1 (and, if needed, read2)

prefix for the read files names, i.e. it will be added in front of the strings in --readFilesIn

format of input read files

number of reads to map from the beginning of the file

clipping options from either end of the mates

Equal/NotEqual - lengths of names,sequences,qualities for both mates are the same / not the same. NotEqual is safe in all situations.

character(s) separating the part of the read names that will be trimmed in output (read name after space is always trimmed)

number to be subtracted from the ASCII code to get Phred quality score