Add remote dataset

Point to a remotely hosted .bumbl index and matching .lengths file. The .bumbl.bi sidecar is assumed at the bumbl URL with .bi appended. Hosts must allow CORS and HTTP Range requests on the bumbl / bi files.

Shredtools extract - HPRC

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Pangenome

Genome

Contig

Start End

— OR —

Region

gzip

Tips

Shredtools runs completely client-side. Downloading large regions across many assemblies may slow down your browser temporarily.

Select a Genome and Contig, then set Start / End, or type a single Region (CONTIG:start-end). The contig dropdown applies to the start/end fields.
I'm Feeling Lucky picks a random assembly and a random ~10–100 kbp window, then runs the query.
On CHM13 or GRCh38, pick a gene from the Gene list to auto-populate the region.
After Build FASTA, click Save FASTA (or Save FASTA.gz) to download.
FASTA download is available for HPRCr2 pangenomes only (hprcv2_enhanced / hprcv2_merged).
The following assemblies are not available for downloading sequences: CN1, I002C, KOREF1, KSA001, and YAO (both haplotypes).
Use the gzip checkbox to shrink large multi-assembly extracts.
Intervals in the Unavailable tab span multiple contigs and are omitted from FASTA output.
Plotting currently works best for small regions (< 2 Mbp). To plot larger regions, use the Shredtools command line tool (GitHub).

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Sequences: loading…

genome	contig	start	end	length
Run a query to populate.

BED (copy from below)

genome	Contig 1	Contig 2
Assemblies spanning multiple contigs will be listed here.

Run a query to see length distribution across selected assemblies.

Run a query, then click Plot to render MUM extract synteny (matplotlib loads on first plot).