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 allo...2193 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 f...hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in...2042 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long read...rt reads to both the contigs and reference genome, and then constructs a novel data str...2190 days ago
ASAR: Advanced metagenomic Sequence Analysis in R
An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pat...2187 days ago
Epiviz: an interactive visualization tool for functional genomics data.
Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other gen...owsers, but allows multiple visualizations of data within genomic regions using...ser-supplied visualizations. It also includes data fro...2187 days ago
transrate: Understanding your transcriptome assembly
Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in det...2183 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
FastANI is developed for fast alignment-free computation of whole-genome Average Nu..., accuracy and potential applications are described here: "High-throughput ANI Analysis of 90K Prokaryotic Genomes Re...2183 days ago
Nanopolis: polish a genome assembly
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs an...2170 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...ed de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy o...le discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the tradition...2170 days ago
nanofilt: Filtering and trimming of long read sequencing data
Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and mapping https://github.com/wdecoster/nanofilt2166 days ago