/usr/share/doc/ssake/examples/README.txt is in ssake-examples 4.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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TEST DATA / SSAKE ASSEMBLIES
A) Testing the distribution with very short reads:
../SSAKE -f Herpesvirus_3.60kb.reads.fa -m 16 -o 2 -w 5 -c 1 -b HStestInstall
B) 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 -u 1 -i 0 -j 20
C) Testing SSAKE on real (experimental) MiSeq sequence data
1) Ebola (Zaire ebolavirus isolate Ebola)
./MiSeqEbolaAssemblyPIPELINE.sh
(read download,trimming,formatting,assembly)
2) Campylobacter showae - CRC tumor isolate / Illumina MiSeq data
./MiSeqCampylobacterAssemblyPIPELINE.sh
(read download,trimming,formatting,assembly)
or
./MiSeqCampylobacterAssembly.sh
(just the assembly)
3) Escherichia coli / 2014 Illumina MiSeq data
./MiSeqEcoliAssembly250XPE300.sh
(just the assembly)
This is illumina MiSeq base space data (one tenth of 2500-fold coverage run)
sequence ~ 250X, 550bp fragments PE300
*compare your assembly to:
coliMiSeq300m80.contigs.stats1
coliMiSeq300m80.scaffolds.stats1
4) Fusobacterium nucleatum - CRC tumor isolate / Illumina HiSeq 2000 data
./HiSeqFusobacteriumAssembly.sh
(read download, assembly)
5) De Novo Targeted assembly of a TMPRSS2:ERG fusion using a prostate adenocarcinoma RNA-seq dataset
./runSSAKEtargeted.sh
(read download,trimming,formatting,assembly)
6) C. elegans linked-read assembly
./CelegansLinkedReadsAssembly.sh
(read download, assembly)
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