MeDuSa: a multi-draft based scaffolder
MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained...ysis (e.g. their phylogenetic relationships) or the availability of paired end read libra...2327 days ago
2377 days ago
Ra assembler - a de novo DNA assembler for third generation sequencing data
Integration of the Ra assembler - a de novo DNA assembler for third generation sequ...ool. Unlike other state-of-the-art assemblers, Ra does not have an error correction step. Instead, it relies...2376 days ago
Seal: SEquence ALignment evaluation suite
Seal is a comprehensive sequencing simulation and alignment tool ev...e alignment algorithms, including: Reading a pre-existing reference g...repeat variability rate). Simulating reads from random locations in the...nt tool and calculating the number of reads that...2369 days ago
Jabba: Hybrid Error Correction for Long Sequencing Reads
Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using se...equences will be corrected (e.g. PacBio reads). The corrections will be written to a f...t is a file in fasta format with corrections of the long reads, and additionally a file in the in...2037 days ago
ECTOOLS: Long Read Correction and other Correction tools
Long Read Correction and other Correction tools This package is a...lection of scripts. To run the correctionroutine se...rtowsk@cshl.edu In short, the correction algorithm takes as input the unitigs from a short read assembly and uses them to correct long read data. More background information f...2367 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 generatio...s. Of course, some long read correction algorithms are better than others, and developers of long read correction algorithms will wish to...2367 days ago
proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contigu...(100-500bp) Unitigs 454, ... proovread maps high coverage data to pacbio reads (bwa mem, blasr, daligner)...2367 days ago
Dot, an interactive viewer for genome-genome comparison
Dot, an interactive dot plot viewer that allows genome scientists to visualize genome-genome alignments in order...file to a more streamlined coordinates file with an index that enables Dot to read in mo...2358 days ago
HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: ...2334 days ago