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.

   Sequence annotated format
       --genbank
              Input file is in genbank format.

       --embl Input file is in embl format.

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

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

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

   ecoPCR related format
       --ecopcr
              Input file is in ecoPCR format.

       --ecopcrdb
              Input is an ecoPCR database.

   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.

AUTHOR

       The OBITools Development Team - LECA

COPYRIGHT

       2019 - 2015, OBITool Development Team

 1.02 12                                   Jan 28, 2019                       OBIJOINPAIREDEND(1)