Thursday, January 19, 2017

New version 3.2.1_01032017

I just posted a new version of the assembler.  The new version includes the following changes:

1. improved ploidy detection for heterozygous genome assembly; now the ploidy is auto-detected and difference settings are used for heterozygous genomes to filter the alternative haplotype
2. improvement in speed and correctness of mega-reads correction of PacBio/nanopore reads; now we require all gaps in mega-reads that are filled with raw PacBio/nanopore reads to have >=3 coverage even for high coverage long read data sets
3. changed local alignment parameters in CA8 overlap/scaffold/consensus to speed up the alignments without apparent loss of sensitivity

Overall the new version should be 10-20% faster and more correct.  The heterozygous genomes will output one haplotype as final assembly in dedup.genome.scf.fasta file.  Both haplotypes are still available in 9-terminator/genome.scf.fasta.

The new version is posted in