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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


No version available


  • person_outline Thomas Otto

Additional information

The software can be downloaded via a Virtual Machine.

Publication for Post-Assembly Genome-Improvement Toolkit

PAGIT citations


Complete Genome Sequence of Agrobacterium tumefaciens 1D1609

Genome Announc
PMCID: 5908930
PMID: 29674541
DOI: 10.1128/genomeA.00253-18

[…] rt, 11,564,340 reads) and one mate pair library (∼4,100-bp insert, 8,219,766 reads). The de novo assembly was performed using AllPaths-LG (). The initial draft assembly was iteratively improved using PAGIT (). In each iteration, the Illumina reads were mapped to the assembly using Burrows-Wheeler Aligner (BWA) (), programmatically checked using SAMtools (), and visually inspected using Integrative […]


Complete Genome Sequence of Spiroplasma floricola 23 6T (ATCC 29989), a Bacterium Isolated from a Tulip Tree (Liriodendron tulipifera L.)

Genome Announc
PMCID: 5908944
PMID: 29674553
DOI: 10.1128/genomeA.00302-18

[…] ary (∼283-bp insert, ∼416-fold coverage) and one mate-pair library (∼4,000-bp insert, ∼476-fold coverage). The initial de novo assembly was performed using ALLPATHS-LG release 52188 (). Subsequently, PAGIT version 1 () was used to assist an iterative process for improving the assembly. For each iteration, the raw reads were mapped to the assembly using BWA version 0.7.12 (), programmatically check […]


Understanding Mucor circinelloides pathogenesis by comparative genomics and phenotypical studies

PMCID: 5955452
PMID: 29436903
DOI: 10.1080/21505594.2018.1435249
call_split See protocol

[…] ormed using SOAPdenovo2 software [] (kmer size of 49). Reads with quality less than 30 over 70% of the read were filtered using NGS QC Toolkit []. Final assembly was generated using ABACAS and IMAGE (PAGIT) [], using Mucor circinelloides CBS277.49 (GenBank assembly accession GCA_001638945.1) as reference. ABACAS was run twice, with an intermediate IMAGE step to close additional gaps. For running I […]


Comparative Genomics and Identification of an Enterotoxin Bearing Pathogenicity Island, SEPI 1/SECI 1, in Staphylococcus epidermidis Pathogenic Strains

PMCID: 5869381
PMID: 29495323
DOI: 10.3390/toxins10030093
call_split See protocol

[…] ory, St Petersburg Academic University, St Petersburg, Russia) with 21-33-55-77-97 k-mers. SPAdes output contigs of < 1000 bp or with coverage of <10× were removed. Sequences were completed using the post-assembly genome-improvement toolkit from the Sanger Institute []. The final sequence annotation was performed with the NCBI genome annotation pipeline. The unique chromosomes for each sequence an […]


Multiple Roots of Fruiting Body Formation in Amoebozoa

Genome Biol Evol
PMCID: 5804921
PMID: 29378020
DOI: 10.1093/gbe/evy011
call_split See protocol

[…] ia and BLASTx for fungi). If a contig had a higher similarity to known bacterial or fungal sequences than to any Amoebozoa genome, it was excluded from the analysis. Further gap closure was done with PAGIT (; last accessed January 31, 2018) using default values. For assembly of the mitochondrial genome, we extended the contig using SSPACE (). The resultin […]


Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates

BMC Genomics
PMCID: 5748942
PMID: 29291727
DOI: 10.1186/s12864-017-4249-6

[…] PAGIT toolkit [] was used to further improve the quality of the assembly by closing gaps on scaffolds, correcting base errors and generate an annotation of CDS based on the reference genome AF2122/97. […]


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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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