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 coverage, repetitive elements and short read length make de novo genome assembly difficult, often resulting in sequence and/or fragment “gaps” – uncharacterized nucleotide (N) stretches of unknown or estimated lengths. Some of these gaps can be closed by re-processing latent information in the raw reads.
Source text:
(Paulino et al., 2015) Sealer: a scalable gap-closing application for finishing draft genomes. BMC Bioinformatics.
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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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