IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer
This package is intended to provide tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer. It includes a functions to generate a number plots...2354 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...nd DALIGNER. Coupled with long-read error correctors and consensus tools, miniasm may also be useful to produce high-quality assemblies. Minimap and miniasm are ultrafast tools for (i) mapping and (ii) asse...2350 days ago
MinION_GC: An R script to do some QC on MinION data
Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single,...2344 days ago
Harvest: a suite of core-genome alignment and visualization tools
...ite of core-genome alignment and visualization tools for quickly analyzing thousan...bination detection, and phylogenetic trees. Tools Parsnp - Core-genome...tion of alignments, trees and variants HarvestTools - Archiving and postproc...2339 days ago
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dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
...ily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes fro...2327 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
...ifferent assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures. https://jgi.doe.gov/data-and-tools/meraculous/ https://arxiv.or...2326 days ago
xmatchview: smith-waterman alignment visualization
xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It all...re written in python and run on linux and windows. They serve as visual tools for analyzing cross_match ali...2319 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
...in the Supporting Online Materials, specifically in the section labelled “Pipeline description”. In addition, the pipeline uses tools and methods from Juicer...2319 days ago
Seal: SEquence ALignment evaluation suite
...from random locations in the genome based on input parameters of read length, coverage, sequencing error rate, and indel rate. Applying alignment tools to the genome and the reads t...2313 days ago