ASAP accepts as input HDF5 files following the LOOM format, developped by Linnarson lab. Note that ASAP complies with 3.0.0 specifications.

ASAP accepts as input HDF5 files (.h5) from CellRanger developped by 10x Genomics [specifications].

ASAP accepts as input simple Plain-text matrices, with as column delimiter tabulation, comma, semi-colon or space. First or last column as gene names is optional. Gene names are then mapped to the Ensembl database. First line as cell/sample names is optional too. The file can be compressed.

ASAP supports archive files that contain several datasets in a plain-text format. You can select which dataset to take as input in the interface.

ASAP supports compressed archive files that contain several datasets in a plain-text format. You can select which dataset to take as input in the interface.

ASAP supports compressed files (zip or gzip).

ASAP requires all three files to be archived/compressed in a single file (.tar, .tar.gz, .gz, .zip, .bz2, .tar.bz2). The files need to be named:

• barcodes.tsv
• genes.tsv or features.tsv
• the main data matrix in a file with extension .mtx. If several mtx files are present, a file named matrix.mtx is required and only this one will be used

From version 8, ASAP supports Seurat objects (rds).