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OBIJOINPAIREDEND(1) OBITools OBIJOINPAIREDEND(1)

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

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

The N first sequence records of the file are discarded from the analysis and not reported to the output file

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

Input file is in genbank format.

Input file is in embl format.

Input file is in fasta format (including OBITools fasta extensions).

Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq sequencers).

Input file is in fastq format produced by Solexa (Ga IIx) sequencers.

Input file is in ecoPCR format.

Input is an ecoPCR database.

Specifying the sequence type

Input file contains nucleic sequences.

Input file contains protein sequences.

OPTIONS TO SPECIFY OUTPUT FORMAT

Standard output format

--fasta-output
Output sequences in OBITools fasta format

Output sequences in Sanger fastq format

Generating an ecoPCR database

--ecopcrdb-output=<PREFIX_FILENAME>
Creates an ecoPCR database from sequence records results

Miscellaneous option

Print sequences in upper case (default is lower case)

COMMON OPTIONS

Shows this help message and exits.

Sets logging in debug mode.

AUTHOR

The OBITools Development Team - LECA

COPYRIGHT

2019 - 2015, OBITool Development Team

July 27, 2019 1.02 13