GapFiller pipeline

GapFiller specifications


Unique identifier OMICS_09433
Name GapFiller
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A pre-assembled scaffold sequences (FASTA) and NGS paired-read data (FASTA or FASTQ).
Output data The final gap-filled scaffolds are provided in FASTA format.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Walter Pirovano <>

Publication for GapFiller

GapFiller IN pipelines

PMCID: 5278652
PMID: 28138345
DOI: 10.7150/jgen.17863

[…] university malaysia genomics facility., illumina adapter removal, whole genome assembly, in-silico scaffolding and gap closing were performed using trimmomatic v0.35, spades v3.6.2, sspace v3.0 and gapfiller v1.10, respectively 6-9. genomic relatedness among different strains was inferred based on average nucleotide identity (ani) using jspecies v1.2.1 10. phylophlan v0.99 was subsequently used […]

PMCID: 5374229
PMID: 28360155
DOI: 10.1128/genomeA.00076-17

[…] using velvet (5). as a result, 7,014,713 reads were assembled in 154 contigs and 12 scaffolds longer than 6 kbp. the longest scaffold resulted in 3.9 mbp. in silico gap filling was performed with gapfiller 1.10 (6), closing 12 gaps and adding 13,149 bp to the scaffolds. the final assembly of b. thuringiensis inta fr7-4 presented a total size of 6,035,547 bp., the 12 scaffolds were compared […]

PMCID: 5522949
PMID: 28729282
DOI: 10.1128/genomeA.01587-16

[…] removed using trimmomatic, version 0.32 (4). afterward the assembly was performed using velvet v1.2.10 (5), with a k-mer value of 41 and a minimum contig size of 500, followed by gapfilling with gapfiller v1.11 (6). annotation was carried out with an in-house pipeline, as described in references 7, 8, followed by additional annotation via priam (9), version march 2013. mapping of reads […]


IMA Genome-F 8

PMCID: 5729718
PMID: 29242781
DOI: 10.5598/imafungus.2017.08.02.10

[…] assembled from trimmed reads using spades v. 3.10 (bankevich et al. 2012) and was further placed into scaffolds using sspace standard v. 3.0 (boetzer et al. 2011). gaps were filled or reduced with gapfiller v. 1.10 (boetzer & pirovano 2012). several runs of genome assembly were conducted using different parameters. assemblies obtained from these runs were subjected to quality […]

PMCID: 5854017
PMID: 29267892
DOI: 10.1093/infdis/jix647

[…] the oxford genomics centre, where libraries were made and dna was sequenced on the ilumina platform. velvet was used to make de novo genome assemblies, which were further improved using sspace and gapfiller [26–28]., the nonpneumococcal streptococcus species data set contained 834 genomes of 69 different streptococcal species (supplementary table 2). thirty-four genomes were newly sequenced […]

GapFiller institution(s)
BaseClear BV, Einsteinweg 5, Leiden, Netherlands

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