Anybody experimented with hybrid assemblies using newbler 2.6?
I fed newbler 1.2 million titanium reads and 2.4 million 100-bp HiSeq2000 v3 reads (a random subset from 12 different treatments of total ~90 million reads). Everything was from cDNA and in fastq format. The result was fine compared to assembly of either set of reads alone. Took about 24 hours on an OK desktop.
About ~13000 contigs from 454, ~26,000 from illumina, 16,000 from hybrid.
Some 5' or 3' fragments in the 454 assembly were complete in the hybrid. Some contigs that were split in two in the illumina assembly were joined in the hybrid. Mapping all 90 million illumina reads onto the hybrid assembly with gsMapper also seemed fine. Took a couple of hours (quick output mode).
Will hopefully get around to doing a comparison with mira.
I fed newbler 1.2 million titanium reads and 2.4 million 100-bp HiSeq2000 v3 reads (a random subset from 12 different treatments of total ~90 million reads). Everything was from cDNA and in fastq format. The result was fine compared to assembly of either set of reads alone. Took about 24 hours on an OK desktop.
About ~13000 contigs from 454, ~26,000 from illumina, 16,000 from hybrid.
Some 5' or 3' fragments in the 454 assembly were complete in the hybrid. Some contigs that were split in two in the illumina assembly were joined in the hybrid. Mapping all 90 million illumina reads onto the hybrid assembly with gsMapper also seemed fine. Took a couple of hours (quick output mode).
Will hopefully get around to doing a comparison with mira.
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