Pilon pipeline

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
Requirements JRE
Maintained Yes



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  • person_outline Bruce Walker <>

Additional information


Publication for Pilon

Pilon IN pipelines

PMCID: 5915480
PMID: 29720997
DOI: 10.3389/fgene.2018.00130

[…] illumina reads were mapped to the canu assembly using bwa v0.7.15-r1140 (li and durbin, 2009). the uniquely mapped reads were filtered using samtools v1.3.1 (li et al., 2009) and passed to pilon v1.17 (walker et al., 2014) to correct remaining snp and small indel errors., the ptt w1-1 reference assembly was scaffolded into chromosomes primarily by matching optical restriction maps […]

PMCID: 5388867
PMID: 28401919
DOI: 10.1038/srep46155

[…] (baseclear bv, leiden, the netherlands). data were mapped to the cen.pk113-7d genome or to in silico-generated plasmid sequences using the burrows-wheeler alignment tool65 and processed with pilon66. identified single-nucleotide differences were inspected with the integrated genomics viewer67 (igv). the chromosomal copy number variance (cnv) was estimated using the poisson mixture model […]

PMCID: 5689209
PMID: 29145861
DOI: 10.1186/s12915-017-0439-6

[…] sequence into additional gaps at one (4698) or both (1152) ends, resulting in 9,084,592 bp of additional sequence in the assembly (additional file 2: table s1). sequence error polishing with pilon [24] corrected 540,621 base substitutions, 791,550 insertions (totaling 1,032,222 bp), and 304,339 deletions (totaling 597,799 bp; additional file 2: table s4), resulting in the final mmur 3.0 […]

PMCID: 4713829
PMID: 26751217
DOI: 10.1371/journal.pntd.0004332

[…] than 200x, reads were down-sampled using picard [54] prior to mapping. variants, including both single nucleotide polymorphisms (snps) and multi-nucleotide polymorphisms, were identified using pilon version 1.5 as described [29] and were used to construct phylogenetic trees using fasttree [55]., we defined lineage-specific variants for lineage x, as those occurring in at least 95% […]

PMCID: 4848111
PMID: 27064254
DOI: 10.1038/ng.3548

[…] using bwa version 0.5.960. in cases where read coverage of the reference was greater than 200x, reads were down-sampled using picard (see urls) prior to mapping. variants were identified using pilon version 1.5 as described61. all sites with unambiguous snps were used to generate a phylogenetic tree using fasttree version 2.1.362. to assess the amount of unexplained phenotypic resistance […]

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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