1099 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
...a perfect map to the reference. Reapr is finicky though, and can’t use libraries with different read lengths, so you’ll have to use assemblies based on the raw data for thi...1334 days ago
2096 days ago
Comment on "Running Trinity on RNA-seq !"
...ctionally annotate the transcripts using Trinotate. If your organism has an assembled genome, consider using the Trinity transcriptome assemblies for gene structure annotation...2120 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...for (i) mapping and (ii) assembly. Designed for long, noisy reads, they do not have a correction or consensus step, and therefore the resulting assemblies are contiguous (i.e. long) bu...2172 days ago
Comment on "Software packages for next gen sequence analysis"
MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data MaGuS (Map-GUided Scaffolding) is a scaffolder and a reference-free ev...2905 days ago
3006 days ago
Comment on "Software packages for next gen sequence analysis"
DNAMAN uses fast alignment algorithms to assemble quickly and accurately a large number of overlapping sequences. This could be a nice tutorial for genome assemblies with overlapping sequences http://www.lynnon.com/pc/assembly.html3237 days ago
Comment on "Software packages for next gen sequence analysis"
Genome assemblies tool and related papers at http://www.plosone.org/browse/Sequence+assembly+tools?startPage=53&filterAuthors=&filterSubjectsDisjunction=&filterA...3240 days ago