Difference between revisions of "PBcR: Polishing the assembly"
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quiver -j 16 /path/to/cmp_h5file.h5 -r /path/to/9-terminator/asm.ctg.fasta -o /path/to/9-terminator/asm.quiver.fasta -o /path/to/9-terminator/asm.quiver.gff | quiver -j 16 /path/to/cmp_h5file.h5 -r /path/to/9-terminator/asm.ctg.fasta -o /path/to/9-terminator/asm.quiver.fasta -o /path/to/9-terminator/asm.quiver.gff | ||
</div> | </div> | ||
| − | Apart from the fofn file, the <span style="font-family:courier new,courier,monospace;">pbalign</span> command uses the <span style="font-family:courier new,courier,monospace;">asm.ctg.fasta</span> file as an input file. This file is found in the assembly output sub-folder <span style="font-family:courier new,courier,monospace;">9-terminator</span> (see here for details). Also, a <span style="font-family:courier new,courier,monospace;">cmp_h5file.h5</span> file is needed. For details, see | + | Apart from the fofn file, the <span style="font-family:courier new,courier,monospace;">pbalign</span> command uses the <span style="font-family:courier new,courier,monospace;">asm.ctg.fasta</span> file as an input file. This file is found in the assembly output sub-folder <span style="font-family:courier new,courier,monospace;">9-terminator</span> (see [[PBcR:_Output_folder_structure|here]] for details). Also, a <span style="font-family:courier new,courier,monospace;">cmp_h5file.h5</span> file is needed. For details, see |
[http://files.pacb.com/software/smrtanalysis/1.4/doc/cmp.h5%20Reference%20Guide.pdf http://files.pacb.com/software/smrtanalysis/1.4/doc/cmp.h5%20Reference%20Guide.pdf]. | [http://files.pacb.com/software/smrtanalysis/1.4/doc/cmp.h5%20Reference%20Guide.pdf http://files.pacb.com/software/smrtanalysis/1.4/doc/cmp.h5%20Reference%20Guide.pdf]. | ||
In addition to the <span style="font-family:courier new,courier,monospace;">cmp_h5file.h5</span> file, the <span style="font-family:courier new,courier,monospace;">quiver</span> program also uses some files from the assembly output sub-folder <span style="font-family:courier new,courier,monospace;">9-terminator</span>. | In addition to the <span style="font-family:courier new,courier,monospace;">cmp_h5file.h5</span> file, the <span style="font-family:courier new,courier,monospace;">quiver</span> program also uses some files from the assembly output sub-folder <span style="font-family:courier new,courier,monospace;">9-terminator</span>. | ||
Latest revision as of 13:45, 30 April 2015
After assembly, the quiver progam can be used to increase the quality of the assembly. This program aligns the corrected reads to the assembly sequences, and improves positions of mismatch. The quiver program is part of the SMRT Analysis package that is installed on Abel. To use it, load the package:
module load smrtanalysis/2.3.0
Use the -h argument to display the quiver help file:
quiver -h
To use this program, you need to create a file-of-filenames (fofn) file. See here for how to create a fofn.txt file.
pbalign --nproc 16 --forQuiver fofn.txt /path/to/9-terminator/asm.ctg.fasta /path/to/cmp_h5file.h5
quiver -j 16 /path/to/cmp_h5file.h5 -r /path/to/9-terminator/asm.ctg.fasta -o /path/to/9-terminator/asm.quiver.fasta -o /path/to/9-terminator/asm.quiver.gff
Apart from the fofn file, the pbalign command uses the asm.ctg.fasta file as an input file. This file is found in the assembly output sub-folder 9-terminator (see here for details). Also, a cmp_h5file.h5 file is needed. For details, see
http://files.pacb.com/software/smrtanalysis/1.4/doc/cmp.h5%20Reference%20Guide.pdf.
In addition to the cmp_h5file.h5 file, the quiver program also uses some files from the assembly output sub-folder 9-terminator.
