DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orde...essor relationships in the ancestor. Then a greedy algorithm is used to reconstruct the an...cies. Computer simulation was used to validate the algori...2203 days ago
2201 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algori...2179 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...ilability of de novo assembly algorithms, it is feasible to study ent...of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome a...elop a transcriptome assembly algorithm that recovers alternatively s...2161 days ago
2161 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and...2158 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...Memory- and time- efficient machine learning algorithms that address these shortcomi...ration of these two technologies. Results: We designed and developed Hercules, the fi...ine learning-based long read error correction algorithm. The algorithm models ever...2112 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
Second generation sequencing technologies paved the way to an exceptional increase in the...a paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algori...2112 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads...ygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algori...2052 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
CSBFinder is a standalone Desktop java application with a graphical user interface, that can also be executed via com...same order, across a wide range of taxa. CSBFinder incorporates an efficient algori...2047 days ago