evigene22may07.tar
------------------
extract to evigene/ with: tar -xf evigene22may07.tar

Update to mainly Gnodes portion of EvidentialGene (evigene22jan14).
Some small corrections to that 1st stable release of Gnodes.
Gnodes is described at http://arthropods.eugenes.org/EvidentialGene/other/gnodes/
with a paper in draft form soon to be available.  

Please comment to me/project if you try out Gnodes, evidentialgene@googlegroups.com 
If you have problems with it, they will be fixed as soon as possible.

NEW:
These scripts are used in Gnodes doc results; some will be
incorporated in later updates to main gnodes_pipleline

scripts/genoasm/gnodes_std2genecov.pl
.. alternate to gnodes_sam2genecov.pl that uses output of samtools depth
   instead of using sam/bam files directly.  It is faster, has some small
   diff with gnodes_sam2genecov.pl, but essentially same calculations.

.. gnodesqwik variants use gnodes_std2genecov.pl, samtools depth,
.. they are faster by 2x or more than main gnodes_pipe methods,
   but are as yet incomplete variants of gnodes_pipe.  An expert may want
   to do as I did, use gnodes_pipe.pl for first run on a given genome assembly,
   then run_gnodesqwik for other DNA samples testing same assembly.
scripts/genoasm/gnodes_work/run_gnodesqwik.sh
scripts/genoasm/gnodes_work/run_gnodesqwik_at1k.sh
scripts/genoasm/gnodes_work/run_gnodesqwik_at1ksw.sh
scripts/genoasm/gnodes_work/run_gnodesqwikvl.sh
.. run kmer and mgse alternate GSE software
scripts/genoasm/gnodes_work/run_gnokmers.sh
scripts/genoasm/gnodes_work/run_gnokmers_at1k.sh
scripts/genoasm/gnodes_work/run_gnokmers_atvlr.sh
scripts/genoasm/gnodes_work/run_testmgse.sh

scripts/genoasm/gnodes_work/run_rdecontam.sh
.. rdecontam.sh removes reads of DNA sample that align to contaminant sequences
scripts/genoasm/gnodes_work/run_srafetchfa.sh
.. fetch SRA readset from NCBI (using sratoolkit)

Updated from 22Jan release:
scripts/genoasm/cds_meanvar.pl
scripts/genoasm/gnodes_chrplot.R
scripts/genoasm/gnodes_covsum.pl
scripts/genoasm/gnodes_pipe.pl
scripts/genoasm/gnodes_sam2covtab.pl
scripts/genoasm/gnodes_sam2genecov.pl
scripts/genoasm/gnodes_sumgenecov.pl