NAME

       illuminapairedend - description of illuminapairedend

       IMPORTANT:
          illuminapairedend replaces solexapairend.

       illuminapairedend  aims at aligning the two reads of a pair-end library sequenced using an
       Illumina platform.

          · If the two reads overlap, it returns the consensus sequence together with its quality

          · Otherwise,  it   concatenates   sequence   merging   the   forward   read   and   the
            reversed-complemented reverse read.

       The program uses as input one or two fastq 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.

       illuminapairedend  align  the  forward  sequence record with the reverse complement of the
       reverse sequence record. The alignment algorithm takes into account the base qualities.
          Example:

              > illuminapairedend -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 aligned
          together and the consensus sequence is stored in the `` seq.fastq`` file.

ILLUMINAPAIREDEND SPECIFIC OPTIONS

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

       --index-file=<FILENAME>

       Filename points to the file containing the illumina index reads

       --score-min=<FLOAT>
              minimum score for keeping alignment. If the alignment score is below this threshold
              both  the  sequences are just concatenated.  The mode attribute is set to the value
              joined.

OPTIONS TO SPECIFY INPUT FORMAT

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

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

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.

ILLUMINAPAIREDEND ADDED SEQUENCE ATTRIBUTES

          · ali_dir

          · ali_length

          · score

          · score_norm

          · mode

          · pairend_limit

          · sminL

          · sminR

          · seq_ab_match

          · seq_a_single

          · seq_b_single

          · seq_a_mismatch

          · seq_b_mismatch

          · seq_a_deletion

          · seq_b_deletion

          · seq_b_insertion

          · seq_a_insertion

AUTHOR

       The OBITools Development Team - LECA

COPYRIGHT

       2019 - 2015, OBITool Development Team

 1.02 12                                   Jan 28, 2019                      ILLUMINAPAIREDEND(1)