Tags: Bioinformatics, Blobsplorer, Visualization, Assembled DNA, Sequence, contigs, Species, Pools.
2867 days ago
npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmi...Tags: npScarf, real-time, scaffolder, SPAdes, contigs, Nanopore, sequencing, reads
2140 days ago
Tags: blasr, download, scaffolder, OPERA-LG, temporarySam, genome, contigs
2136 days ago
mScaffolder: A comparative genome scaffolding tool
A comparative genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the candidate genome guided by their alignments to th...Tags: mScaffolder, comparative, genome, scaffolding, tool, genome, contigs, scaffolds
2136 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of ...Tags: CAT/BAT, tool, taxonomic, classification, contigs, metagenome, assembled, genomes, MAGs
1433 days ago
Tags: BIGMAC, Breaking, Inaccurate, Genomes, Merging, Assembled, Contigs, Long, Read, Metagenomic, Assembly
2525 days ago
SuRankCo: supervised ranking of contigs in de novo assemblies
SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet. https://bm...Tags: SuRankCo, Supervised, Ranking, Contigs, Assemblies
2523 days ago
SCUBAT: Scaffolding Contigs Using Blat And Transcripts
SCUBAT (Scaffolding Contigs Using BLAT And Transcripts) uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.Tags: SCUBAT, Scaffolding, Contigs, Blat, Transcripts
2230 days ago