SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.
1) Support large kmer up to 127 to utilize long reads. Three version are provided.
I. The 31mer version support kmer only <=31.
II. The 63mer version support kmer only <=63 and doubles the memory consumption than 31mer version, even being used with kmer <=31.
III. The 127mer version support kmer only <=127 and double the memory consumption than 63mer version, even being used with kmer <=63.
Please notice that, with longer kmer, the quantity of nodes would decrease significantly, thus the memory consumption is usually smaller than double with shifted version.
For more information, look at the MANUAL in /usr/share/doc/soapdenovo2 or on soapdenovo web site.
AUTHOROlivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging