Does number of supercontigs matters for assembly.? i got a 40 MB fungal genome sequence assembly with ~12500 supercontigs by velvet software.?( more than no. of genes present) how can i validate it?
-
Last edited by Pinal; 09-26-2012, 11:05 AM. -
Dear Pinal,
What command/parameters have you used for the assembly? what data do you have single or paired end? what is the Insert size if it is paired end? Have you trimmed the low quality reads?
best wishes,
RahulRahul Sharma,
Ph.D
Frankfurt am Main, Germany -
That's about 3200bp average contig size. You should probably only count contigs above a certain size. Velvet default is 2*K-1, which is often a bit low. 12,500 doesn't sound great, but it's not a disaster, but I would expect better. How many reads do you have? What length? Paired? You may not have enough coverage.Comment
-
NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM -
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM
Comment