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) usi...ram of k-mer occurrences from a sequence file. Adds metadata in o...d K-mers between two (or three) sequence files or hashes. sect:...r each sequence in the assembly.SEquence Coverage estimator Tool....1974 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-base...2098 days ago
2083 days ago
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 trade-offs betw...in these reads. Using datasets from two DNA-seq BAC clones (CH17-157L1 and CH...227A2), and human brain cerebellum polyA RNA-seq, we show that Hercules-correc...2077 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...ram could utilize Illumina Paired-end RNA-sequencing reads from target spec..._scaffolder ) for scaffolding genome sequences. The most important fea...2060 days ago
Qualimap2: Evaluating next generation sequencing alignment data
...mmand-line interface to facilitate the quality control of alignment sequencing data and its derivatives...ounts. Supported types of experiments include: Whole-genome sequencing Whole-exome sequencing RNA-seq (speica...2056 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Rainbow is developed to provide an ultra-fas...assembling short reads produced by RAD-seq. First, Rainbow clusters read...rozygote while discriminate repetitive sequences. At last, Rainbow uses...sed on simulation and a real guppy RAD-seq data, we show that Rainbow is...2018 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS requires two input files: Draft assembly fasta file Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)1958 days ago
GeneOverlap: An R package to test and visualize gene overlaps
Overlapping gene lists can reveal biological meanings and may lead to novel hypothese...with gene activation and its genome-wide enrichment can be mapped by using ChIP-seq experiments. Because of its a...1948 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
...XCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines...e package for the detection of copy number variants (CNVs) from whole-exome sequencing data.EXCAVATOR has bee...1940 days ago