PBcR: Polishing the assembly

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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


In addition to the cmp_h5file.h5 file, the quiver program also uses some files from the assembly output sub-folder 9-terminator.