HTTPS and S3 links to genomic index files freely available in the AWS cloud
| Home |
|---|
| Bowtie |
| HISAT |
| Kraken/Bracken |
| Centrifuge |
| SPUMONI |
| SPUMONI 2 |
SPUMONI (GitHub repo) is a fast read classification tool for targeted nanopore sequencing. It uses a compressed r-index together with a streaming matching-statistics algorithm and statsitical test to classify reads.
The exact accession ids used for the reference genomes in the Zymo mock community indexes can be found here (s3 link).
| Collection | Date | HTTPS URL | S3 URL |
|---|---|---|---|
| Zymo mock community, one genome, matching strain | March, 2021 | positive.spumoni, null.spumoni | positive.spumoni, null.spumoni |
| Zymo mock community, one genome, non-matching strain | March, 2021 | positive.spumoni, null.spumoni | positive.spumoni, null.spumoni |
| Zymo mock community, pan-genome, with matching strain | March, 2021 | positive.spumoni, null.spumoni | positive.spumoni, null.spumoni |
| Zymo mock community, pan-genome, without matcing strain | March, 2021 | positive.spumoni, null.spumoni | positive.spumoni, null.spumoni |
| Human, one genome (T2T CHM13 v1.0) | March, 2021 | positive.spumoni, null.spumoni | positive.spumoni, null.spumoni |
| Human, three genomes (T2T CHM13 v1.0, Ashv2.0, GRCh38) | March, 2021 | positive.spumoni, null.spumoni | positive.spumoni, null.spumoni |
SPUMONI is the work of Omar Ahmed, Massimiliano Rossi, Sam Kovaka, Michael C. Schatz, Travis Gagie, Christina Boucher, and Ben Langmead.