Abstract
The increasing accessibility and reduced costs of sequencing has made genome analysis accessible to more and more researchers. Yet there remains a steep learning curve in the subsequent computational steps required to process raw reads into a database-deposited genome sequence. Here we describe “Genomer,” a tool to simplify the manual tasks of finishing and uploading a genome sequence to a database. Genomer can format a genome scaffold into the common files required for submission to GenBank. This software also simplifies updating a genome scaffold by allowing a human-readable YAML format file to be edited instead of large sequence files. Genomer is written as a command line tool and is an effort to make the manual process of genome scaffolding more robust and reproducible. Extensive documentation and video tutorials are available at http://next.gs.
Highlights
The decreasing costs and increasing diversity of high-throughput sequencing methods is making genome analysis a common method to tackle unresolved questions in microbiology [1]
Manual curation of a genome sequence and corresponding annotations may still improve upon the results of automated methods
The large size of FASTA sequence files or general feature format (GFF) annotation files makes changing these in a text editor difficult
Summary
The decreasing costs and increasing diversity of high-throughput sequencing methods is making genome analysis a common method to tackle unresolved questions in microbiology [1]. Editing a genome sequence or annotation is nontrivial and requires effort on a researcher’s part. The large size of FASTA sequence files or general feature format (GFF) annotation files makes changing these in a text editor difficult. Tasks such as organising project files, adding additional sequences to an assembly, updating incorrect annotations or preparing files for database deposition all divert effort from the main goal of analysing a genome.
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