PAGIT statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PAGIT

Tool usage distribution map

This map represents all the scientific publications referring to PAGIT per scientific context
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Associated diseases

This word cloud represents PAGIT usage per disease context

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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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