cli

Running abstar from the command line is designed to be relatively straightforward, even for users with minimal experience with command-line applications. In the most basic case, with a single input file of human antibody sequences, abstar can be run with:

abstar run path/to/sequences.fasta path/to/output/

abstar will process all sequences contained in sequences.fasta and the results, including annotations and logs, will be deposited into path/to/output/.

Note

If path/to/output/ does not exist, it will be created.

If you have a directory of FASTA/Q-formatted files for abstar to process, you can pass a directory instead of a single file, and all files in the directory will be processed:

abstar run path/to/input/ path/to/output/

additional options

abstar has many other options that can be used to customize the resulting analysis or to handle more complex cases. This includes:

• merging paired-end reads prior to annotation

• UMI detection and incorporation into the annotated output

• creation and use of custom germline databases

• different output file formats for AIRR-compatible annotations