Web Apollo: a web-based genomic annotation editing platform
Web Apollo is the first instantaneous, collaborative genomic annotation...ing technology is that there are more and more researchers sequencing n...ew genomes. These researchers require tools to...Chrome or Firefox) to jointly analyze and precisely describe the features...2479 days ago
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
We developed a prokaryotic genome annotation pipeline, DFAST, t...an on-line annotation server, and to date, over 7,000 jobs have...hich is also available as a standalone command-line program. Th...he annotation workflow easily and will...ions and incorporation of new tools in the future. Availability...2370 days ago
poRe: an R package for the visualization and analysis of nanopore sequencing data
Motivation: The Oxford Nanopore MinION device represents a uniqu...atics community will need to design and build a suite of tools specifically for MinION dat...to manipulate, organize, summarize and visua...t/projects/rpore/ . A tutorial and further information are availab...2361 days ago
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 O...task. However, nanopore sequencing is an emerging and rapid...ation of metrics that we haven’t thought of, and welcome feedback at mike.s...2361 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...s 9 out of 12 PacBio datasets and 3 out of 4 ONT datasets into...iasm assembly (on the X axis) and the HGAP3 assembly (on Y). Th...rror correctors and consensus tools, mi...map and miniasm are ultrafast tools for (i) mapping and (ii) asse...q reads.fq # Install minimap and miniasm (requiring gcc and zlib...2357 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 computation...2350 days ago
Harvest: a suite of core-genome alignment and visualization tools
Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial g...lls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome...2346 days ago
2343 days ago
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
While the number of sequenced diploid genomes have been steadily increasing in the la...ns challenging. As a result, there is a shortage of tools for...embling HP genomes were proposed in the pre-NGS era and are not well suited for NGS pro...2333 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
Meraculous is a whole genome assembler for Next Generation Sequencing d...utilizing lightweight data structures and multi-threaded parallelizatio...eline implements a highly transparent and porta...ctures. https://jgi.doe.gov/data-and-tools/meraculous/ https://arxiv.or...2333 days ago