I am comparing the genomes of experimentally evolved bacterial populations. I have only been comparing my de novo assembled genomes; these genomes are in fasta format (assembled using SOAPdenovo) and therefore have a multitude of tools to visualize different comparisons (Mauve, Artemis Comparison Tool, etc.). However, I was wondering if I could compare (and visualize comparisons between) genomes that were assembled through reference mapping and are in SAM/BAM format. Any recommended tools?
IGV could be a good option to visualize reference based assembled genome. IGV supports BAM file formate.
Use this browser: http://epigenomegateway.wustl.edu/
Other browsers you could use are: Jbrowse (very common), CLC genomics workbench (nice browser but slow), and the Geneious v9 browser (very good from what I've seen).
I have experienced with IGV, you can also compare mapping of multiple samples to the same reference. It gives you visualization at the resolution upto a single base.
Alternatively you can also try SeqMonk though I never used this but its provided by Babraham Bioinformatics.
UCSC browser can also be useful if you have your data online.
'Tablet' developed by the James Hutton Institute (https://ics.hutton.ac.uk/tablet/) is very intuitive and easy to visualize SAM files. Geneious is also an excellent option but its not free; Tablet is free to download. I prefer using it over IGV or Artemis, or online browsers.
I would prefer IGV to visualize BAM/SAM files for reference based assembly.
Thank you for the suggestions. I think I will be using IGV and Genenious for now since both of them seem to do a good job.
IGV gives you a lot of useful features in addition to visualizing the aligned BAM. You can view multiple BAMs (i.e. samples) at once. You can import feature files (e.g. BED or GFF) so if you are interested in specific regions or genes you can easily jump to them. View paired end reads by read orientation, insert size and other criteria which lets you assess your alignment visually and even spot structural rearrangements.
I am not sure how memory efficient Tablet is, but I managed to load the Loblolly Pine genome (21 GB genome!) as a reference genome in IGV on my desktop with 16 GB RAM.
Unfortunately, I am having trouble with the visualization of the data in IGV, after importing BAM file I get the message "Cannot add sequence that already exists in SAMSequenceDictionary: null". Any ideas?
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools