Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms can lead to...A-seq BAC clones (CH17-157L1 and CH17-227A2), and human brain cerebellum polyA RNA-seq, we show that Hercules-correc...2104 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 Pacific Biosciences SMRT error model. Reads are simulated from both s...2102 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 suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target spec...2086 days ago
Qualimap2: Evaluating next generation sequencing alignment data
Qualimap 2 is a platform-independent application written in Java and R that pro...es of experiments include: Whole-genome sequencing Whole-exome sequencing RNA-seq (speical mode available) ChI...2082 days ago
funannotate: Eukaryotic Genome Annotation Pipeline
Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small e...2074 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
Quality assessment of this mRNA Transcript Assembly Software is described in EvidentialGene_quality. Too many transcript assemblies is much better than too few. I...2062 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 produced by RAD-seq. First, Rainbow clusters reads...2044 days ago
Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a d...ecalled reads not the raw fast5 files (which Deepbinner requires). You have a small/s...2005 days ago
Genome sequence-based (sub-)species delineation.
The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also...1990 days ago
GeneOverlap: An R package to test and visualize gene overlaps
Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pa...1974 days ago