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Gap closing software tools | De novo genome sequencing data analysis

While next-generation sequencing technologies have made sequencing genomes faster and more affordable, deciphering the complete genome sequence of an organism remains a significant bioinformatics challenge, especially for large genomes. Low sequence…
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SPAdes
Desktop

SPAdes

A single-cell assembler for capturing and sequencing “microbial dark…

A single-cell assembler for capturing and sequencing “microbial dark matter” that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes…

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SOAPdenovo
Desktop

SOAPdenovo

Provides a short-read assembly method that can build a de novo draft assembly…

Provides a short-read assembly method that can build a de novo draft assembly for the human-sized genomes. SOAPdenovo is specially designed to assemble Illumina GA short reads. It creates new…

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GMcloser
Desktop

GMcloser

Closes gaps with a preassembled contig set or a long read set (i.e.,…

Closes gaps with a preassembled contig set or a long read set (i.e., error-corrected PacBio reads). GMcloser uses likelihood-based classifiers calculated from the alignment statistics between…

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GapBlaster
Desktop

GapBlaster

A graphical application to evaluate and close gaps. GapBlaster was developed…

A graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. GapBlaster uses contigs obtained in the assembly of the genome to perform an alignment…

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BugBuilder
Desktop

BugBuilder

Can carry out assembly and analysis of microbial genome sequences. BugBuilder…

Can carry out assembly and analysis of microbial genome sequences. BugBuilder takes sequence reads as inputs and produces submission-ready annotated genome assemblies, with ease-of-use prioritised to…

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GAPPadder
Desktop

GAPPadder

Finds and uses reads that originate from repeate-related gaps. GAPPadder is a…

Finds and uses reads that originate from repeate-related gaps. GAPPadder is a sensitive approach for closing gaps on draft genomes with paired-end reads and mate-paired reads. It takes advantage of…

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IMAGE
Desktop

IMAGE Iterative Mapping and Assembly for Gap Elimination

An approach to raise the quality of draft assemblies towards finished, but…

An approach to raise the quality of draft assemblies towards finished, but without manual intervention, using local assemblies of reads from gap regions. IMAGE utilises the large number of sequences…

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GapFiller
Desktop

GapFiller

A stand-alone program for closing gaps within pre-assembled scaffolds.…

A stand-alone program for closing gaps within pre-assembled scaffolds. GapFiller is unique in offering the possibility to manually control the gap closure process. By using the distance information…

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Sealer
Desktop

Sealer

An automated finishing application that uses the succinct Bloom filter…

An automated finishing application that uses the succinct Bloom filter representation of a de Bruijn graph to close gaps in draft assemblies, including that of very large genomes. Sealer has broad…

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FGAP
Web
Desktop

FGAP

An efficient tool to find regions to fill gaps of draft genome sequences. FGAP…

An efficient tool to find regions to fill gaps of draft genome sequences. FGAP demands low computational resources, the results can be easily analyzed by the output generated, and it can be used for…

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OMACC
Desktop

OMACC Optical-Map-Assisted Contig Connector

Closes the gaps between scaffolded contigs with a higher accuracy compared with…

Closes the gaps between scaffolded contigs with a higher accuracy compared with a similar tool. OMACC is advantageous because it takes into account gap size carefully via rescaling optical map and…

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G4ALL
Desktop

G4ALL Graphical contig analyzer for all sequencing platforms

A computational tool integrated with a database that allows the curation and…

A computational tool integrated with a database that allows the curation and extension of contigs produced by de novo assemblers, and the production of a scaffold, even when there is little overlap…

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FinIS
Desktop

FinIS

Allows users to close gaps in the genome assembly as well as validate the…

Allows users to close gaps in the genome assembly as well as validate the genomic scaffold. FinIS considers all gaps simultaneously to find gap sequences that best match the read data and to…

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