GapFiller protocols

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GapFiller specifications

Information


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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Maintainer


  • person_outline Walter Pirovano <>

Publication for GapFiller

GapFiller in pipelines

 (56)
2018
PMCID: 5786695
PMID: 29371369
DOI: 10.1128/genomeA.01565-17

[…] reads were filtered per the read qualities. the reads were then assembled using the spades software (). contigs obtained were combined by use of sspace () and assisted by manual finishing and gapfiller (). this yielded a 7,306,349-bp draft genome sequence with a 66.35% gc content, composed of 14 scaffolds and 14 contigs. open reading frames (orfs) were predicted using prodigal () […]

2018
PMCID: 5814502
PMID: 29449406
DOI: 10.1128/genomeA.01604-17

[…] of 683,373 paired-end reads, filtered per the read qualities, were assembled using the spades software (). the resulting contigs were combined by use of sspace () assisted by manual finishing and gapfiller (). this yielded a 5,614,132-bp draft genome with a 68.24% gc content, composed of 8 scaffolds and 12 contigs. open reading frames (orfs) were predicted using prodigal () with default […]

2018
PMCID: 5908923
PMID: 29674548
DOI: 10.1128/genomeA.00291-18

[…] mass spectrometry (). reads issued from sequencing genomic dna by miseq technology (illumina, inc., san diego, ca, usa) were assembled using spades (), and contigs were combined by using sspace (), gapfiller (), and manual finishing. this analysis yielded 8 scaffolds and 23 contigs. then, genomic dna was sequenced using the minion device and an sqk-lsk108 kit (oxford nanopore, oxford, uk) […]

2018
PMCID: 5908941
PMID: 29674534
DOI: 10.1128/genomeA.00212-18

[…] representation for strain s-137 was 6.98%. a total of 866,229 paired-end reads were filtered per read qualities and assembled using spades software (). contigs were combined by using sspace (), gapfiller (), and manual finishing using similarity searches and synteny block detection., the strain s-137 draft genome was assembled into 25 scaffolds composed of 142 contigs, with a total size […]

2017
PMCID: 5374229
PMID: 28360155
DOI: 10.1128/genomeA.00076-17

[…] using velvet (). 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 (), 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 […]


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GapFiller in publications

 (233)
PMCID: 5924567
PMID: 29690652
DOI: 10.3390/genes9040225

[…] number of contigs, and the length of the largest contig. scaffolding of the selected assembly was performed using sspace [] and the removal of possible gaps present in scaffolds was performed using gapfiller []. homopolymer errors were corrected manually using consed []. the purity of the scaffolds was also checked against the genome of t. aegyptius dsm 12793. possible miss-assemblies […]

PMCID: 5908796
PMID: 29674608
DOI: 10.1038/s41467-018-03968-5

[…] (https://github.com/tseemann/velvetoptimiser). an assembly improvement step was applied to the assembly with the best n50 and contigs were scaffolded using sspace and sequence gaps filled using gapfiller. automated annotation was performed using prokka v1.11., whole-genome metagenomic sequencing was performed on the illumina hiseq 2500 as described previously with human contaminating reads […]

PMCID: 5908923
PMID: 29674548
DOI: 10.1128/genomeA.00291-18

[…] mass spectrometry (). reads issued from sequencing genomic dna by miseq technology (illumina, inc., san diego, ca, usa) were assembled using spades (), and contigs were combined by using sspace (), gapfiller (), and manual finishing. this analysis yielded 8 scaffolds and 23 contigs. then, genomic dna was sequenced using the minion device and an sqk-lsk108 kit (oxford nanopore, oxford, uk) […]

PMCID: 5902063
PMID: 29617440
DOI: 10.1371/journal.ppat.1006966

[…] by refining, ordering, and concatenating the best draft assembly in the sc. a second de novo assembly was generated with spades and assemblies were then merged using zorro []. after this, sspace and gapfiller were used to scaffold the assembly and remove ns [,]. final contigs were ordered using mauve, manually curated using act, and concatenated []. filtered illumina reads from isolates […]

PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] de novo by velvetoptimiser v.2.2.5 []. the optimized k-mer, expected coverage and coverage cutoffs were obtained through iterative process for various k-mer (37 to 67). gaps were minimized by gapfiller v.1.10 [] using original reads via 15 iterations (−m 50, −o 3)., the assembled contigs of re-sequenced isolates were aligned to the reference assembly by nucmer in mummer v.3.23 [] […]


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

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