Download - Oshlack/JAFFA GitHub Wiki

Latest JAFFA release

Download the latest (or older) releases from the github release page:

https://github.com/Oshlack/JAFFA/releases/

Reference files

You will also need one of these supporting reference files:

Default:

JAFFA_REFERENCE_FILES_HG38_GENCODE22.V2.tar.gz - Files for hg38 (JAFFA 1.07+ assumes this reference by default)

hg19 and mm10 are also supported, but require you to follow the instructions here in addition to downloading the reference below

JAFFA_REFERENCE_FILES_HG19_GENCODE19.tar.gz - Files for hg19
JAFFA_REFERENCE_FILES_MM10_GENCODEVM4.tar.gz - Files for mouse (mm10)

Please see FAQandTroubleshooting if you would like to generate your own reference files for JAFFA (e.g. for an unsupported genome).

Datasets

Demo data - See Example for running the demo

Simulations from our papers:

BEERS (no fusions) - BEERS_1.fastq.gz BEERS_2.fastq.gz
MiSeq (120 fusions) - MiSeqSim_1.fastq.gz MiSeqSim_2.fastq.gz MiSeqSim_truth.tar.gz
ONT and PacBio (2500 fusions) - LongReadFusionSimulation.tar.gz

Versions prior to 1.06 that are not hosted on github#

JAFFA_1.05.tar.gz - Fusion gene names are now ordered by fusion gene orientation (previously gene names were listed alphabetically)

JAFFA_1.04.tar.gz - This version fixes an issue that caused the direct mode to be slow on some large dataset.

JAFFA_1.03.tar.gz - Major improvements over 1.0 such as:

Reads that map to intronic, intergenic, and chrM regions are now first filtered out before running the pipeline. This improves the RAM and time requirements for the assembly and hybrid modes.
For the direct mode we now calculate spanning pairs
fusions classed as PotentialRegularTranscripts are no longer reported
we now threshold on 2 spanning reads for LowConfidence fusions (previously this was 1), to help remove library prep false positives.

JAFFA_1.0.tar.gz -This version is identical to 0.91. Improvements of 0.9 are that it works out the read length itself and includes a few bug fixes and checks. Thanks to Aliaksei Holik for correcting the bug in the spanning pairs calculation.

JAFFA_0.9.tar.gz