Thomas D. Otto

REAPR: a universal tool for genome assembly evaluation

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

Abstract Advances in sequencing technology allow genomes to be sequenced at vastly decreased costs. However, the assembled data frequently are highly fragmented with many gaps. ...

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

Abstract Motivation: The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, w...

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

BamView: viewing mapped read alignment data in the context of the reference sequence

Abstract Summary: BamView is an interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome seq...