Ribbon is a long-read genome alignment visualizer that is online at genomeribbon.com Use Ribbon to visualize alignments and variants, showing detailed alignments for each read and with powerful filtering and sorting options. Ribbon and this tutorial were created by Maria Nattestad with sponsorship from Pacific Biosciences. Go to genomeribbon.com to put in your own data and try it out live!

1. 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

2. Ribbon tutorial
Loading 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

3. 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

4. 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 variants
BEDPE is for long-range variants with two breakpoints

5. 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)

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

7. 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

8. Filter which
pieces of the
reference are
shown

9. Select a read
by clicking on
it up here
And it will show
up down here

10. 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

11. Filter by any column

12. Multiple
filters can
be active
at once
Sort by
clicking on
column
names

13. Use =, >, or <