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| #!/bin/bash | |
| ##### | |
| # This script shows how the simulated reads are generated in the paper. | |
| # All training datasets are downloaded from ENA and processed with poretools. | |
| # Only 2D pass reads are extracted and stored on bcgsc ftp server. | |
| ##### | |
| ##### Download the source file | |
| mkdir NanoSim | |
| cd NanoSim | |
| wget https://github.com/bcgsc/NanoSim/archive/master.zip | |
| unzip master.zip | |
| # After this step, you should have a folder called NanoSim, and inside you have master.zip and NanoSim-master two sub-folders | |
| ##### Inside NanoSim, create a working directory | |
| mkdir ecoli_simulation | |
| cd ecoli_simulation | |
| # 1. E. coli R7 dataset | |
| # Origin: ftp://climb.genomics.cn/pub/10.5524/100001_101000/100102/Ecoli_R7_CombinedFasta.tgz | |
| # Get the 2D reads | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/ecoli_R7_2D.fasta | |
| # Get the reference genome | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/ecoli_K12_MG1655_ref.fa | |
| # Profiling stage, make sure to set the mode of read_analysis.py to -r-x or above | |
| ../NanoSim-master/src/read_analysis.py -i ecoli_R7_2D.fasta -r ecoli_K12_MG1655_ref.fa -o ecoli | |
| # Simulation stage, suppose the genome to be simulated is called test.fasta and make sure to provide the correct path to it | |
| ../NanoSim-master/src/simulator.py circular -r test.fasta -c ecoli # Note the -c option has to be the same as -o in read_analysis.py, or both use default parameter | |
| # To get the profile directly: | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/ecoli_R7_profile.zip | |
| # 2. E. coli R7.3 dataset | |
| # Origin: http://www.ebi.ac.uk/ena/data/view/ERX708228, ERX708229, ERX708230, ERX708231 | |
| # Get the 2D reads | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/ecoli_R73_2D.fasta | |
| # Get the reference genome | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/ecoli_K12_MG1655_ref.fa | |
| # To get the profile directly: | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/ecoli_R73_profile.zip | |
| # 3. E. coli UCSC phase1b dataset | |
| # Origin: http://www.ebi.ac.uk/ena/data/view/ERP010368 | |
| # Get the 2D reads | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/ecoli_UCSC_phase1b_2D.fasta | |
| # Get the reference genome | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/ecoli_K12_MG1655_ref.fa | |
| # To get the profile directly: | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/ecoli_UCSC1b_profile.zip | |
| # 4. S. cerevisiae dataset | |
| # Origin: http://labshare.cshl.edu/shares/schatzlab/www-data/nanocorr/2015.07.07/W303_ONT_Raw_reads.fa.gz | |
| # Get the 2D reads | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/yeast_2D.fasta | |
| # Get the reference genome | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/yeast_S288C_ref.fa | |
| # To get the profile directly: | |
| wget ftp://ftp.bcgsc.ca/supplementary/NanoSim/yeast_profile.zip | |