obijoinpairedend: Joins paired-end reads

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.

Sequence annotated format

--genbank

Input file is in genbank format.

--embl

Input file is in embl format.

Specifying the sequence type

--nuc

Input file contains nucleic sequences.

--prot

Input file contains protein sequences.

Options to specify output format

Standard output format

--fasta-output

Output sequences in OBITools fasta format

--fastq-output

Output sequences in Sanger fastq format

Generating an ecoPCR database

--ecopcrdb-output=<PREFIX_FILENAME>

Creates an ecoPCR database from sequence records results

Miscellaneous option

--uppercase

Print sequences in upper case (default is lower case)

Common options

-h, --help

Shows this help message and exits.

--DEBUG

Sets logging in debug mode.