2321 days ago
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...2326 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
...ht data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on commodity clusters in under a day. The process pipeline implements a highly transpare...2311 days ago
2305 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
...bly procedure is described in detail in the Supporting Online Materials, specifically in the section labelled “Pipeline description”. In addition, the pipeline uses tools and methods from&n...2303 days ago
LRCstats: Long Read Correction Statistics
LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced...2296 days ago
PGAP-X: Extension on pan-genome analysis pipeline
PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze...2277 days ago
HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
...to reproduce results in the paper can be found in this repository. HINGE is an OLC(Overlap-Layout-Consensus) assembler. The idea of the pipeline is shown below....2262 days ago
Generate interactive codon usage plots
Generate interactive codon usage plots as used at ensembl.lepbase.org. The input file format can be generated from an Ensembl database using the export_json.pl script from the easy-import pipeline. live demo2242 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and...833 days ago