Wednesday, September 27, 2017

MaSuRCA hybrid assembly strategy and recent results on Illumina and Oxford Nanopore data video presentation

I have just uploaded to YouTube ( my presentation on the latest MaSuRCA mega-reads results on assembly of Illumina and Oxford Nanopore MinION human genome data.  In this presentation I describe a de novo human genome assembly of NA12878 data set with N50 contig size of over 1Mb from $10000 worth of sequencing data and outline MaSuRCA mega-reads strategy.

Friday, September 15, 2017

New version MaSuRCA 3.2.3

I have just finished testing the new version of MaSuRCA, version 3.2.3.  The only new notable added feature in the new version is gap closing for assemblies that use PacBio/Oxford Nanopore data.  The other changes are all improvements related to stability, usability and speed:

1. Added scaffold gap closing for hybrid assemblies that use PacBio/Oxford Nanopore
2. Improved the speed and stability of filter for Illumina mate pairs
3. Ploidy and Estimated genome size for the genome are now saved and can be read from ESTIMATED_GENOME_SIZE.txt and PLOIDY.txt files.
4. run Nucmer multi-threaded when SoapDenovo2 used as contigger/scaffolder, for filtering out redundant small contigs after gap closing.
5. updated MUMmer to the latest version
6. many small performance improvements to avoid re-running steps if they have been run on assembler re-start

The new version is available from my ftp site: