PAGIT

Genome projects now produce draft assemblies within weeks owing to advanced
high-throughput sequencing technologies. For milestone projects such as
Escherichia coli or Homo sapiens, teams of scientists were employed to manually
curate and finish these genomes to a high standard. Nowadays, this is not
feasible for most projects, and the quality of genomes is generally of a much
lower standard. This protocol describes software (PAGIT) that is used to improve
the quality of draft genomes. It offers flexible functionality to close gaps in
scaffolds, correct base errors in the consensus sequence and exploit reference
genomes (if available) in order to improve scaffolding and generating
annotations. The protocol is most accessible for bacterial and small eukaryotic
genomes (up to 300 Mb), such as pathogenic bacteria, malaria and parasitic worms.
Applying PAGIT to an E. coli assembly takes approximately 24 h: it doubles the
average contig size and annotates over 4,300 gene models.

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

PAGIT is a tool to improve the quality of genomes that have already been assembled. It performs subsequent steps needed from the point of contig assembly, which includes closing gaps, error correction of consensus sequence and use other closely related reference genomes to scaffold and generate annotation. PAGIT bundles the software ABACAS, IMAGE, iCORN and RATT.

PAGIT

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