2185 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types": Refere...which an RNAseq experiment is performed. It allows reads to be aligned against the ref...ilable. In this case one would need to assemble the reads into transcripts using de nov...2185 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...ng K-mers from another sequence file. blob: Given, reads and an assembly, calculates b...compare two K-mer hashes produced by different NGS reads. profile: Creates a K-mer co...2034 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 reads. ReMILO aligns the initial sh...ddition, ReMILO also aligns the contigs to long reads and find their differences fr...2182 days ago
transrate: Understanding your transcriptome assembly
Transrate is software for de-novo transcriptome assembly quality analysis....embly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for...2175 days ago
Merqury: reference-free quality and phasing assessment for genome assemblies
Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual....1481 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
ARC is a pipeline which facilitates iterative, reference...asing accuracy of results by only considering those reads which should assemble togethe...nally difficult problem of assembly by breaking the reads into small, manageable subset...2162 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/nanofilt2158 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (...2077 days ago
2143 days ago