Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such high error rate...2409 days ago
phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for common...2409 days ago
PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison metho...2407 days ago
dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
...uipe-Elements-transposables-.html?lang=en You can find the original publication in GBE here: https://academic.oup.com/gbe/article/7/4/1192/533768 output examples of...2406 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, small, .t...2405 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
...When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared wi...2402 days ago
jobTree based python wrapper to run the genome simulation tool suite Evolver
evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolv...2400 days ago
2396 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
...ly or in unison on a wide variety of architectures. https://jgi.doe.gov/data-and-tools/meraculous/ https://arxiv.org/ftp/arxiv/papers/1703/1703.09852.pdf2388 days ago
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions
TRRUST contains 8,444 and 6,552 TF-target regulatory relationships of 800 human TFs and 828 mouse TFs, r...mation of mode of regulation (activation or repression). Currently 8,972 (59.8%) regulatory relationships...2387 days ago