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create a rough scaffold using ion torrent MP reads
Perl
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LICENSE.txt
README
ionPairer.pl
scaffolder.pl

README

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       Scrimpy way to scaffold an assembly using ion torrent reads.

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  Usage:

     Take your existing assembly, bin out the contigs of interest and then
run bwa-long twice (once for each of the forward and reverse reads) to map your
ion MP reads against your contigs.

    Then simply run ionPairer.pl script. There are a few hard-coded options lurking
within but the up and up is that it will detect pairs, wrongly mapped regions
unpaired reads etc. It can determine orientation and insert size automagically.

    The most useful output is a .gv file which you can use to visualise the 
pairings using graphviz. Use this visualisation to remove spurious pairings and
redraw etc. This script is quite useful for making rough scaffold maps.

    Once edited the .gv file, use the scaffolder.pl script to create the scaffolds.
The script will orient the contigs (forward or reverse complement) and scaffold 
the contigs with 25 Ns between each contig.
    
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Project home page

Info on the source tree, documentation, issues and how to contribute, see

http://github.com/minillinim/ionPairer

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Cite

This software is currently unpublished.

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Copyright © 2012 Michael Imelfort. See LICENSE.txt for further details.

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