Commit 83012ff7 authored by Andreas Tille's avatar Andreas Tille
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New upstream version 4.0

parent ba3d8aae

SSAKE

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SSAKE-readme.pdf

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SSAKE-readme.txt→readme.md

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test/CelegansLinkedReadsAssembly.sh

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d=`date`

echo ----------------------------------------------------------------------------------- 

echo Running SSAKE assembly pipeline 

echo ------------------------------------------------------------------------------------ 

echo Downloading trimmed/formatted data on $d ...

echo ------------------------------------------------------------------------------------

rm -rf celegans_paired.fa

wget ftp://ftp.bcgsc.ca/supplementary/SSAKE/celegans_paired.fa.gz

gunzip celegans_paired.fa.gz

echo ------------------------------------------------------------------------------------

echo done. Initiating SSAKE assembly

echo ------------------------------------------------------------------------------------

time ../SSAKE -f celegans_paired.fa -p 1 -m 20 -w 5 -b celegansLR

echo ------------------------------------------------------------------------------------

echo done. Computing stats from contigs

echo ------------------------------------------------------------------------------------

../tools/getStats.pl celegansLR_contigs.fa 500 > celegansLR_contigs_stats.txt

echo done. Computing stats from scaffolds 

echo ------------------------------------------------------------------------------------

../tools/getStats.pl celegansLR_scaffolds.fa 500 > celegansLR_scaffolds_stats.txt

echo assembly pipeline complete. Results are under celegansLR.

test/Herpesvirus_3.60kb.reads.fa

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