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
ftp://ftp.genome.umd.edu/pub/MaSuRCA/latest/
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
ftp://ftp.genome.umd.edu/pub/MaSuRCA/latest/
