CoLoRMap: Correcting Long Reads by Mapping short reads
...otic and eukaryotic. However, short reads are difficult to assemble and...e recent developments in long reads sequencing methods offer a pr...leverage the high quality of short reads to correct errors in long rea...ovel ideas: using a classical shortest path algorithm to find a s...2142 days ago
SimLoRD: A read simulator for third generation sequencing reads
SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the P...ic Biosciences SMRT error model. Reads are simulated from both stran...ructure is respected when drawing reads. (Simulation of genome rearra...ding to number of passes Outputs reads i...2140 days ago
LRCstats: a tool for evaluating long reads correction methods
LRCstats is an open-source pipeline for benchmarking DNA long rea...orrection algorithms for long reads outputted by third generation...d by Pacific Biosciences. The reads produced by third generation...ed by Illumina. However, long reads are plagued by high error rat...ng methods or using accurate, short r...2140 days ago
LoRMA: A tool for correcting sequencing errors in long reads
An error correction method that uses long reads only. The method consists of two phases: first, w...length of k-mers, and second, the corrected reads are further polished using lo...d method is the most accurate one relying on long reads o...2124 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
Added Command line argument support. Multi-stage execution modes. Support for paral...lization. Now execution proceeds in batches of long reads the size of which can be set...Added utilities folder. Added support for multiple short r...2125 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is su...for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads f...2124 days ago
Rebaler: program for conducting reference-based assemblies using long reads.
Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I m...2113 days ago
2110 days ago
rHAT: a seed-and-extension-based noisy long read alignment tool
rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.2108 days ago
Heatmapper: web-enabled heat mapping for all
Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface....2100 days ago