I am looking for a way to align contigs from a de novo assembly against a reference genome and visualize which parts of the genome are covered. Any recommendations?
Thanks
Thanks
-
-
I really like Tablet (http://bioinformatics.oxfordjournals...t/btp666v1.pdf) as a genome viewer. I believe it supports ACE, AFG, MAQ, SOAP and SAM formats. -
But Tablet is for viewing individual contigs from assemblies on their own (looking at the reads within a contig).
The question was about comparing the contigs of an assembly against a reference genome. This has similarities to comparing different genomes... maybe ACT (the Artemis Comparison Tool) would be suitable?
Comment
-
We used BLASTn to map ca 2000 contigs against various references.
Visualisation of contig position and the annotated genes in that region was with the R package GenomeGraphs.
I would really recommend this and can send an example script if you pm me with your email address.Comment
-
What is your average contig length? For contigs assembled from short reads I have been using " bwa bwasw"
It natively produces SAM format which your can convert to BAM and directly view in Tablet/IGVComment
-
mummer may be best optionComment
-
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, detection...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