Commit 537e951e by Frédéric Boyer

Edited the doc

parent dcda77f7
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.. include:: ../optionsSet/inputformat.txt
:py:mod:`obisample` specific options
.. cmdoption:: -s <INT>, --sample-size <INT>
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.. include:: ../optionsSet/inputformat.txt
:py:mod:`obitail` specific options
.. cmdoption:: -n <INT>, --sequence-count <INT>
Created on 30 dec. 2009
:py:mod:`solexaPairEnd` : align overlapping pair-end solexa reads and return the consensus sequence together with its quality
.. codeauthor:: Eric Coissac <>
:py:mod:`solexaPairEnd` aims at aligning the two reads of a pair-end library sequenced using a Solexa.
The program takes for arguments one or two fastq solexa sequences reads files.
In the case where two files are given one should be associated with the -r option. Sequences corresponding to the same read pair must have the same line number in the two files.
In the case where one file is provided, sequences, which are supposed to be all of the same length, are considered to be the concatenation of the two pair end reads. Hence
the first half of a sequence is considered one extremity of the pair-end and the second half the other one.
:py:mod:`solexaPairEnd` align the first sequence with the reverse complement of the second sequence and report the consensus sequence of the alignment (taking into account
the base qualities) together with the qualities for each base of the reported consensus sequence.
.. code-block:: bash
> solexaPairEnd -r seq3P.fasta seq5P.fasta > seq.fasta
@author: coissac
from obitools.options import getOptionManager
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