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reference-free ddRADseq analysis tools
branch: master
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.gitignore updated .gitignore to include gdata build directory
101013_lane7_sample_data.csv added test sample data csv
DB_index_by_well.csv DB_index_by_well.csv added
LICENSE lgpl3 added prepro
README README updated add iterative
USAGE_NOTES Update USAGE_NOTES 20120208 radtag_denovo code added 20120208 radtag_denovo code added add iterative corrected add iterative tagged version added add iterative 20120208 radtag_denovo code added
gdata-2.0.10.tar.gz added gdata 2.0.10 multiple subject support added, bugfixes 20120208 radtag_denovo code added iterative_rtd updates rtd fixes 20120208 radtag_denovo code added fixed sq lookup add iterative add add pool passthough for db records in legacy lookup refactored vcf_to_rqtl read_quality_statistics added commit exception on 0 length return
s_7_sequence-1M.txt.gz added sample sequence data DB_index_by_well.csv added simulation scripts updated to include efficiency predictions 20120208 radtag_denovo code added switched .uniqued handling to compressed by default Merge branch 'master' of added htseq style vcf_to_rqtl ( prepro


pipeline script generates reference-sorted, indexed BAM from uniqued reads from radtag sequencing lanes.

To generate uniqued reads, see

four accessory programs and three python libraries are used, listed below.
for parallel execution, GNU parallel is also HIGHLY recommended. 
Experimental LSF support is also available.

-        PATH must contain: blat mcl mcxload muscle samtools [parallel]
-  PYTHONPATH must contain: numpy gdata editdist

see (at the time of this writing, March 09 2011)
  GNU parallel

  numpy *
  gdata        install gdata v2.0.10 included in this repository
			(recent versions are known to be incompatible
			with rtd code, but are available at:

* N.B. numpy is also available as part of the excellent Enthought Python Distribution,
available free for academic/non-profit use at

It appears as of this writing (June 2012) the google spreadsheets API only correctly queries 
all fields of a user-edited spreadsheet if the first column is blank.
column A is therefore left blank in the tables generated by
(I recommend hiding column A of all programmatically accessed GDoc spreadsheets)
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