/usr/share/doc/ssake/examples/README.txt is in ssake-examples 3.8.2-1.
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Testing the distribution with very short reads:
../SSAKE -f Herpesvirus_3.60kb.reads.fa -m 16 -o 2 -w 5 -c 1
Testing the targeted assembly using a seed/target sequence:
../SSAKE -f Herpesvirus_3.60kb.reads.fa -m 16 -o 2 -w 5 -b seedtest -c 1 -s Herpesvirus_3.60kb.seed.fa -i 1 -j 20
Testing SSAKE on real (experimental) MiSeq sequence data for CRC tumor isolate
Campylobacter showae:
./MiSeqCampylobacterAssemblyPIPELINE.sh
(read download,trimming,formatting,assembly)
or
./MiSeqCampylobacterAssembly.sh
(just the assembly)
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