NAME

obijoinpairedend - description of obijoinpairedend

obijoinpairedend aims at joining the two reads of a paired-end library.

For this purpose, it concatenates sequence merging the forward read and the reversed-complemented reverse read.

The program uses as input one or two sequences reads files.

If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files.
If just one file is provided, sequence records are supposed to be all of the same length. The first half of the sequence is used as forward read, the second half is used as the reverse read.

Example:

> obijoinpairedend -r seq3P.fastq seq5P.fastq > seq.fastq

The seq5P.fastq sequence file contains the forward sequence records. The seq3P.fastq sequence file contains the reverse sequence records. Pairs of reads are joined together and the resulting sequence is stored in the `` seq.fastq`` file.

OBIJOINPAIREDEND SPECIFIC OPTIONS

-r <FILENAME>, --reverse-reads=<FILENAME>: Filename points to the file containing the reverse reads.

OPTIONS TO SPECIFY INPUT FORMAT

Restrict the analysis to a sub-part of the input file

--skip <N>: The N first sequence records of the file are discarded from the analysis and not reported to the output file

--only <N>: Only the N next sequence records of the file are analyzed. The following sequences in the file are neither analyzed, neither reported to the output file. This option can be used conjointly with the –skip option.