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GapFiller specifications


Unique identifier OMICS_12013
Name GapFiller
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ (.gz, .bz2), FASTA (.gz, .bz2), SAM, BAM
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Francesca dalin

Publication for GapFiller

GapFiller citations


Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus

R Soc Open Sci
PMCID: 5936940
PMID: 29765675
DOI: 10.1098/rsos.172212

[…] SPACE []. In the initial assemblies, 76% of gaps in scaffolds (3592/4754) were closed in for L. guyanensis LgCL085, 63% (4096/6530) for L. naiffi LnCL223 and 67% (4834/8786) for L. braziliensis using Gapfiller []. Erroneous bases were corrected by mapping reads to the references with iCORN [] (electronic supplementary material, figure S12). Misassemblies detected and broken using REAPR [] were ali […]


Pathogenic adaptations of Colletotrichum fungi revealed by genome wide gene family evolutionary analyses

PLoS One
PMCID: 5915685
PMID: 29689067
DOI: 10.1371/journal.pone.0196303

[…] ipt to remove low quality reads (N > 10%, or sQ ≤ 5) and reads with adaptor contamination. Clean reads were then de novo assembled using the AbySS assembler version 1.3.5 [], with a Kmer value of 50. GapFiller version 2.0 [] was used to further fill gaps and generate scaffolds. The generated genome assembly was deposited at GenBank under accession no. MVNS00000000.Repetitive DNA elements were pred […]


Draft Genome Sequence of Lactobacillus fermentum NCDC 400, Isolated from a Traditional Indian Dairy Product

Genome Announc
PMCID: 5764951
PMID: 29326227
DOI: 10.1128/genomeA.01492-17

[…] genomic data ().The present study utilized paired-end sequencing using the Illumina HiSeq 2500 platform and identified a total of 17,733,506 high-quality (HQ) reads by Velvet, KmerGenie, SSPACE, and GapFiller. The final assembly of 138 scaffolds, with an N50 of 27,950 bp, maximum scaffold size of 101,072 bp, and genome size of 1.89 Mb, showed the relative genome length in comparison with those of […]


Draft Genome Sequence of the Filamentous Fungus Hypoxylon pulicicidum ATCC 74245

Genome Announc
PMCID: 5764932
PMID: 29326208
DOI: 10.1128/genomeA.01380-17

[…] reads was 25 bp. De novo assembly was performed using SPAdes (version 3.5.0) with the default parameters, using a kmer range of 39 to 127, and scaffolding was performed using SSPACE version 1.10 and GapFiller version 3.0. The final assembly consisted of 204 contigs over 500 bp with an average length of 203,162 nucleotides. The total number of nucleotide residues was 41,444,948, with a GC content […]


Draft Genome Sequence of a Red Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed

Genome Announc
PMCID: 5754502
PMID: 29301893
DOI: 10.1128/genomeA.01429-17
call_split See protocol

[…] 99, and 127). Contigs shorter than 500 bp or that comprised fewer than four reads were subsequently filtered out of the assembly. Assembly improvement was attempted using a combination of SSPACE and GapFiller ().Draft assembly of the whole genome yielded 78 contigs, with an N50 value of 333,942 bp. The genome of BJB412 is predicted to be 6,786,668 bp in length, which is comparable to that of othe […]


Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs

Sci Rep
PMCID: 5741766
PMID: 29273719
DOI: 10.1038/s41598-017-18374-y

[…] Read tool, which selects and uses only the longest PacBio reads to construct a scaffolding. Finally, the gap size between pairs of contig was calculated (lower than 5-Kb in all cases) and closed with Gapfiller, using the distance information derived from the paired-read data.The contigs generated from the Illumina sequencing reads were aligned to the de novo assembled chromosomes using LAST aligne […]


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GapFiller institution(s)
Department of Mathematics and Computer Science, University of Udine, Udine, Italy; IGA Applied Genomics Institute, Udine, Italy; Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
GapFiller funding source(s)
Progetto Bandiera Epigenomica “EPIGEN”

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