BLASR maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and
the genome. The first set of alignments is found by querying an index of the reference genome, and then refining until only
high scoring alignments are retained. Additional pulse metrics are loaded into the resulting cmp.h5 file to enable downstream
use of the Quiver algorithm.
Using DAG-based consensus algorithm, pre-assemble long reads as the first step of the Hierarchical Genome Assembly process
(HGAP). Version 2 is a stepping stone for scaling to much larger genomes.
p_assembleunitig.merSize
14
p_assembleunitig.defaultFrgMinLen
500
p_assembleunitig.moduleName
P_AssembleUnitig
p_assembleunitig.ovlMinLen
40
p_assembleunitig.libraryName
pacbioReads
p_assembleunitig.specTmpl
analysis/etc/celeraAssembler/unitig.spec
p_assembleunitig.description
This module runs Celera Assembler v8.1 to the unitig step, then finishes with our custom unitig consensus caller
p_assembleunitig.genomeSize
7000000
p_assembleunitig.ovlErrorRate
0.06
p_assembleunitig.xCoverage
15
p_assembleunitig.maxSlotPerc
1
p_assemblypolishing.moduleName
P_AssemblyPolishing
p_assemblypolishing.description
Polish a pure-PacBio assembly for maximum accuracy using the Quiver algorithm.