2148 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 allows reads to be...2148 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. The k-mer spectrum of this read set can be used for independently ev...1444 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...data. ARC decomplexifies the traditionally difficult problem of assembly by breaking the reads into small, manageable subsets which can then be assembled quickly and efficiently in pa...2124 days ago
2098 days ago
Referee: Genome assembly quality scores
...ever all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site in an assembled genome to calculate a quality...2023 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
...h sequence quality and contiguity, handles low-level contamination in reads, is fast, and produces an identical assembly for the same input when assembled multiple times with the same...2014 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, ra...1981 days ago
1959 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
...od, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (with s...1945 days ago