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 Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or ra...2139 days ago
LRCstats: a tool for evaluating long reads correction methods
LRCstats is an open-source pipeline for bench...reads outputted by third generation sequencing technology such as machines p...reads produced by third generation sequencing technology, as the name sugge...reads outputted by next generation sequencing technologies to correct long...2139 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, we use an iterative alignment-free correction method based on de Bruijn gr...2124 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...suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies....2124 days ago
Qualimap2: Evaluating next generation sequencing alignment data
Qualimap 2 is a platform-independent application writt...ce to facilitate the quality control of alignment sequencing data and its derivatives like...ted types of experiments include: Whole-genome sequencing Whole-exome sequencing RNA-...2120 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
MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies
MimicrEE2, a multi-threaded Java program for genome-wide forward simulations of evolving populations. MimicrEE2 enab...sed in E&R studies and offers a wide range of different adaptive models (selective...2102 days ago
nQuire: a statistical framework for ploidy estimation using next generation sequencing
nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens,...2097 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it wo...2096 days ago