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Gennady Fedonin edited this page May 2, 2017 · 4 revisions

To run VirGenA with test data download and unzip release files.

on Windows:

You can set number of threads in config_test_win.xml by changing value of ThreadNumber element.

Using Windows command promt change dir to unzipped folder and type:

java -cp ./VirGenA.jar RefBasedAssembler config_test_win.xml

on Linux:

You can set number of threads in config_test_linux.xml by changing value of ThreadNumber element.

Change permissions of ./tools/usearch8.1.1861_i86linux32 to make it executable. After that using shell change dir to unzipped folder and type:

java -cp ./VirGenA.jar RefBasedAssembler config_test_linux.xml

Tets data is an artificial mixture containing 100000 HIV reads of three different subtypes (01_AE, B and C) in equal proportions. VirGenA should detect these components and assemble genome-length consensus sequences for all components.

Results will be stored in ./res/ folder. Expected output is:

  1. Files (fasta) with assemblies of three mixture components named after the selected references: 01_AE.TH.90.CM240.U54771_assembly.fasta, B.FR.83.HXB2_LAI_IIIB_BRU.K03455_assembly.fasta, C.BW.96.96BW0502.AF110967_assembly.fasta
  2. Sorted bam files with read alignments and corresponding index files (bai): 'reference_name'_mapped_reads.bam and 'reference_name'_mapped_reads.bai
  3. Log file.

How to run SSPACE scaffolder on the resulting assembly

  1. Download https://github.com/nsoranzo/sspace_basic
  2. Download https://github.com/gFedonin/VirGenA/blob/master/bin/GenerateTabFile.class and place it in the release directory.
  3. Run from the release directory: java -cp ./VirGenA.jar:. GenerateTabFile -in ./res/ -out ./res/sspace/ -c ./config_test_linux.xml
  4. Run SSPACE: perl pathToSSPACE/SSPACE_Basic_v2.0.pl -l ./res/sspace/res.lib -s ./res/sspace/res_contigs.fasta -x 0

Expected output:

All SSPACE output will be in the current directory, including standard_output.final.scaffolds.fasta, which contains resulting scaffolds. In this particular case SSPACE does not join contigs to scaffolds, printing all 4 initial contigs with new names.

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