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This file enumerates the test files in this directory.
README.txt This file.
hg18L*E*Q*.fasta These 15 files contain reads generated from the hg18 full reference genome.
The reads were generated with wgsim from the Wellcome Trust Sanger Institute.
The number following the "L" indicates the read length.
The number following the "E" indicates the error percentage.
The number following the "Q" indicates the number of reads.
RandomSV_Events.fasta This file contains reads generated by wgsim on a set of SV event contigs created by SVsim.
There are 10,000 SV events of varying lengths in random genome locations on hg18,
with equal numbers of local inversions, duplication, deletions, and distal insertions.
wgsim was used to generate 500-mer reads for the above events
with 2% error rate at 5X read coverage.
RandomSV_Events.sim.bedpe The bedpe file generated by SVsim that describes the breakpoints in the above .fasta file.
RandomSV_Events.sim The input file to SVsim used to generate the above using the following command:
SVsim -i RandomSV_Events.sim -r <hg18_full.fa> -c 500 -n 25 -p 500 -l -o RandomSV_Events.sim
Alu_Insertions.fasta Similar to RandomSV_Events.fasta except that SVsim was used to create 10,000 Alu insertion events.
Read generation with wgsim is as above.
Alu_Insertions.sim.bedpe The bedpe file generated by SVsim that describes the breakpoints in the above .fasta file.
Alu_Insertions.sim The input file to SVsim used to generate the above using the following command:
SVsim -i Alu_Insertions.sim -r <hg18_full.fa> -c 500 -n 10 -p 500 -l -o Alu_Insertions.sim
CGR_Events.E*.fasta These files each contain 1500 Complex Genome Rearrangement events generated with SVsim.
- The E0 file was generated directly with SVsim. Each contig is approximately 30 kilobases in length.
- The E1 file is a mutated copy of the E0 file with an error rate of 1%, 10% of which are small indels.
- The E4 file is a mutated copy of the E0 file with an error rate of 4%, 90% of which are small indels.
CGR_Events.sim.bedpe The bedpe file generated by SVsim that describes the breakpoints in the above .fasta files.
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