PAGIT pipeline

PAGIT specifications


Unique identifier OMICS_23172
Alternative name Post-Assembly Genome-Improvement Toolkit
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Thomas Otto <>

Additional information

The software can be downloaded via a Virtual Machine.

Publication for Post-Assembly Genome-Improvement Toolkit

PAGIT citations

PMCID: 3998919

[…] was followed for the illumina data. the resulting 454 and illumina reads were de novo assembled using mira. this initial assembly was subsequently improved using approaches described in the pagit protocol [51]. in brief, the contigs were aligned to the wmel genome using abacas [52], creating one large scaffold that consisted of the contigs successfully mapped to the wmel genome […]

PMCID: 4094930

[…] n50 value, while maintaining an expected level of coverage above 20, as described previously [35]. scaffolds were then generated using sspace2 [62], which were subsequently improved using the post assembly genome improvement toolkit (pagit) pipeline [63]. sequence alignments were performed using blat [64] with default settings and displayed using act [65]. the ice displayed in figure  2 […]

PAGIT institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, UK; WeatherallInstitute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
PAGIT funding source(s)
Supported by the European Union 7th framework EVIMalaR and by the Wellcome Trust [Grant number: 098051].

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