Pilon protocols

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Pilon specifications


Unique identifier OMICS_14553
Name Pilon
Alternative name PilonGrid
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Input genome and aligned read files
Input format FASTA, BAM
Output data A modified genome including all single-base, small indel, gap filling, mis-assembly and large-event correction from the input genome.
Output format FASTA
Operating system Unix/Linux, Mac OS
Programming languages Java, Scala
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.21
Stability Stable
Maintained Yes



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  • person_outline Bruce Walker <>

Additional information


Publication for Pilon

Pilon in pipelines

PMCID: 5762679
PMID: 29321680
DOI: 10.1038/s41598-017-18910-w

[…] were subsequently polished using nanopolish (https://github.com/jts/nanopolish) combined with bwa-mem. the polished genome of strain wch96200 was cured by quality-trimmed illumina reads using pilon with default settings, to eventually obtain a more accurate assembly., nucleotide sequence accession numbers. draft whole-genome sequences of isolates wchec1837, wchec96200 and wchec99540 […]

PMCID: 5765654
PMID: 29325559
DOI: 10.1186/s12915-017-0457-4

[…] assembled chromosomal sequences were quality checked using short read data available for each of the strains (ncbi short read archive accessions srs383142, srs383143, and srs383146). we used the pilon procedure to map illumina short reads and corrected indels and snps detected in the illumina read alignments []. see plissonneau et al. [] for more details on the snp calling, map construction, […]

PMCID: 5790871
PMID: 29404424
DOI: 10.1128/mSystems.00108-17

[…] (). we used samtools v 1.2 () and picard tools (https://broadinstitute.github.io/picard/) for sorting, format conversion, and addition of read group information. variants were identified using pilon v 1.16 (). a detailed description of the reference guided assembly pipeline is available at https://github.com/pepperell-lab/rgapeppipe. we removed isolates with mean coverage less than 20×, […]

PMCID: 5815585
PMID: 29451876
DOI: 10.1371/journal.pone.0192452

[…] the “de novo assembly” option of the clc genomics workbench version 9.5.1 (qiagen). mis-assemblies and nucleotide disagreement between the illumina data and the contig sequences were corrected with pilon version 1.20 []. subsequently, the contigs were linked and placed into scaffolds, where the orientation, order and distance between them were estimated using the insert size […]

PMCID: 5897800
PMID: 29650583
DOI: 10.1128/genomeA.00295-18

[…] score, 30; minimum length, 50) (). reads were de novo assembled using spades version 3.9.1, with k-mer lengths of 21, 33, 55, and 77 (). the resulting contigs (>1,000 bp) were outputted to pilon version 1.22 to correct single-nucleotide polymorphisms (snps) and indels (). the resulting contigs were then ordered against a closely related complete l. pneumophila genome with mauve aligner […]

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Pilon in publications

PMCID: 5946035
PMID: 29748397
DOI: 10.1128/genomeA.00229-18

[…] involved preassembly, de novo assembly with celera assembler, and polishing with quiver (). illumina reads were used to improve the genome contiguity, with the help of the error correction software pilon version 1.16 (). the complete circular genome contained two contigs, consisting of one chromosome of 2,632,932 bp (71.3-fold coverage) and the plasmid psgair0252 of 41,662 bp (18.63-fold […]

PMCID: 5946051
PMID: 29748401
DOI: 10.1128/genomeA.00351-18

[…] of sequenced bases was 1,418,902,495. for de novo assembly, canu v1.5 was used with the default parameters; the genome correction step was performed by using illumina data, with the support of pilon v1.18 software (, ). this assembly yielded an average of 2,715,947 bp. the genome was completely assembled by contigs and not by scaffolds. subsequently, the estimated genome size of 5.42 mb […]

PMCID: 5931751
PMID: 29732401
DOI: 10.1126/sciadv.aao1478

[…] xt kit and sequenced on the miseq at a depth of ~2 million reads per sample. to identify polymorphisms, reads were aligned with bwa using the bwa-mem algorithm (). alignments were processed with pilon ()., data from our previously published whole-cell proteomic analysis of m. tuberculosis h3rv were reanalyzed to identify posttranslationally modified peptides (). spectra were searched […]

PMCID: 5920167
PMID: 29700138
DOI: 10.1128/genomeA.00219-18

[…] the mitochondrial contig was first trimmed at both ends to remove overlapping extremities. to improve the quality of the minion sequencing, the assembly was polished using two strategies, (i) the pilon version 1.21 hybrid method () to directly correct the assembly using the illumina reads by five iterative correction steps and (ii) a prior polishing of the sequence by nanopolish (), followed […]

PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] [] and paired-end reads with concordant alignments were selected with samtools view 0.1.19-96b5f2294a [] for error correction. a final genome assembly error correction (polish) was conducted using pilon [] version 1.16 (additional file )., whole genome assembly sequence and gene annotation was publicly available for ptr isolate bfp (genbank accession aaxi01000000). sequence reads for dw7 […]

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Pilon institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA; VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
Pilon funding source(s)
This project has been funded in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No.:HHSN272200900018C. This project has been also funded in part with Federal funds from the National Human Genome Research Institute, National Institutes of Health, Department of Health and Human Services, under grant U54HG003067.

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