Results for "assemblies"
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Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-08...Tags: Circlator, automated, circularization, genome, assemblies, sequencing, reads
2176 days ago
- GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap closure. We demonstrate with sequencing data from...
Tags: GMcloser, close, gaps, assemblies, accurately, likelihood-based, selection, contig, long-read, alignments, Genome, Assembly
2149 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, first run the following commands: cd SALSA m...Tags: SALSA, tool, scaffold, long, read, assemblies, Hi-C, Genome
2145 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in output for easy plotting. gcp: K-mer GC Pr...Tags: KAT, K-mer, analysis, toolkit, quality, control, NGS, datasets, genome, assemblies
1975 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together. Reducing/removing reference bias as compared to mapping...Tags: ARC, pipeline, facilitates, iterative, reference, guided, de novo, assemblies
2104 days ago
GFinisher: a new strategy to refine and finish bacterial genome assemblies
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar GenomeFinisher.jar \ -i target_contigs.fasta \ ...Tags: GFinisher, strategy, refine, finish, bacterial, genome, assemblies
2104 days ago
Rebaler: program for conducting reference-based assemblies using long reads.
Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the task of testing basecallers). It should in pri...Tags: Rebaler, program, conducting, reference-based, assemblies, long, reads, ont, pacbio
2050 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for the...Tags: Synima, Synteny, imaging, tool, annotated, genome, assemblies
2008 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handles low-level contamination in reads, is fast,...Tags: SKESA, strategic, k-mer, extension, scrupulous, assemblies, genome, assembly
1993 days ago
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of principle by creating a genome graph of seven ethnical...Tags: NovoGraph, building, whole, genome, graphs, long-read-based, de novo, assemblies
1992 days ago
