ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...researchers develop a transcriptome assembly algorithm that recovers alternatively spliced isoforms and expression levels while utilizing as many RNA-Seq libraries as possible that co...2132 days ago
2132 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experiment is performed. It all...2132 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist:...1980 days ago
REVIGO: Reduced Visualize gene ontology
REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based...2104 days ago
2089 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...s this to correct errors in these reads. Using datasets from two DNA-seq BAC clones (CH17-157L1 and CH17-227A2), and human brain cerebellum polyA RNA-seq, we show that Hercules-correc...2084 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...2082 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...itable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target spec...2066 days ago
Qualimap2: Evaluating next generation sequencing alignment data
...ng data and its derivatives like feature counts. Supported types of experiments include: Whole-genome sequencing Whole-exome sequencing RNA-seq (speical mode available) ChI...2062 days ago