HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, incl...2369 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads...2369 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 (Newi...2367 days ago
SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.2361 days ago
MeDuSa: a multi-draft based scaffolder
MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained...analysis (e.g. their phylogenetic relationships) or the availability of paired end read...2299 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new...ic relationships among the draft and reference genomes and libraries of paired-end reads...2279 days ago
2235 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling mu...lgorithm that can be proved preserving all phasing paths from reads and paired-end reads...2216 days ago
2188 days ago
Cerulean: A hybrid assembly using high throughput short and long reads
Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genome...2188 days ago