Ribbon is a long-read genome alignment visualizer

For complex variants

For MUMmer assembly/genome alignments

For long-range translocations

Dot plot mode

By Maria Nattestad, sponsored by Pacific Biosciences

Ribbon tutorialLoading a BAM file and using a VCF file to show variants

Ribbon is a long-read alignment visualizer created by Maria Nattestad and sponsored by Pacific Biosciences.

Tutorial created by Maria Nattestad

Load alignments in SAM, BAM, or coordinates format:• SAM: Only choose small files (less than 10MB) where

you want to see all the alignments, or paste in a few lines from the SAM file

• BAM files can be very large but must be sorted and indexed (using Samtools). Ribbon uses code from bam.iobio to fetch reads in the BAM file at certain locations. Using a BAM file means you need to know what locations to look at.

• Coordinate files can be made by MUMmer’s show-coords utility to see genome-genome alignments, but any alignment file can be coerced into this format

• Note: SAM/BAM files must have SA tags indicating the other alignments for each record, otherwise only the main alignment on each line of the file can be shown which would be quite boring

Header of the BAM file was used to draw the reference chromosomes

Or you can type in a position manually here

Upload variants here

Variant types:BED and VCF are single-location variantsBEDPE is for long-range variants with two breakpoints

We loaded a VCF file, and now the contents are shown in this table.

The table allows sorting and filtering.(more details in a few slides)

Click a row to jump to that variant and fetch reads in that region from the BAM file

Now we have loaded all the reads in that region and are showing all their alignments across the whole genome

Variants:

Whole reference:

Relevant pieces of the reference, showing reads in forward and reverse directions

Tons of filtering options to try out in this panel.

Details on a single read

Filter which pieces of the reference are shown

Select a read by clicking on it up here

And it will show up down here

Orient the reads by the main alignment at your variant’s location

The variant you selected

Note the thick black bar, that’s the location we picked in the BAM file

Filter by any column

Multiple filters can be active at once

Sort by clicking on column names

Use =, >, or <