Three New Tools to Dramatically Improve Draft Genome Assemblies

Directed Sanger finishing of draft genome sequences is tedious, time consuming and expensive.  However, for the many draft genome sequences being generated using new sequencing technologies users of the data still long for such high quality contiguous sequences. 

The BCM-HGSC has developed PBJelly, Atlas-Link and Atlas-GapFill to automatically improve draft genomes and is using these methods to create better quality genomes.

 We report here the latest results of these improvements, including application to many genomes sequenced with second generation technologies and/or mixed technologies.  These new and existing genomes include the I5k pilot insects, sooty mangabey, baboon, walrus, killer whale, echinoderms, as well as the high quality rat draft genome.  The combined use of these programs results in a doubling of the average contig N50, and increase in thee scaffold N50 stats of 30%. The resulting improvements in sequence contiguity directly benefits downstream analysis especially gene annotation, synteny analysis and assessment of genomic features and functions. We additionally report where to access and how to use these tools.