asap-o-matic

asap-o-matic provides the ability to process ASAP-seq FASTQs for downstream processing and counting of the antibody-dependent reads using Salmon Alevin.

A heavily modified version of asap_to_kite.

About

ASAP-seq uses a few tricks to bridge the oligo sequences attached to CITE-seq/Total-seq antibodies with the oligo tails on the beads of 10x Genomics scATAC-seq kits; however, the reads produced don't match anything that Cellranger understands how to count. asap-o-matic reformats those reads so that they appear like those coming from the feature library of a 10x Genomics scRNA-seq library.

Installation

The easiest way is to run via uv:

uv tool install asap-o-matic

Alteratively, it can be installed using pip

pip install asap-o-matic

or uv:

uv pip install asap_o_matic

Requirements

• Python >= 3.11
  • currently, asap-o-matic is tested against 3.11-3.14
• Rust
• R1/R2/I1/I2 files output by bcl-convert/bcl2fastq or the R1/R2/R3/I3 produced by cellranger mkfastq

Usage:

asap-o-matic [OPTIONS] COMMAND [ARGS]...

Options :

• -f, --fastqs DIRECTORY: Path of folder created by mkfastq or bcl2fastq; can be comma separated that will be collapsed into one output [required]
• -s, --sample TEXT: Prefix of the filenames of FASTQs to select; can be comma separated that will be collapsed into one output [required]
• -o, --id TEXT: A unique run id, used to name output. [required]
• -a, --fastq_source [cellranger|bcl-convert]: Name of the program used to convert bcls to FASTQs. Cellranger mkfastq creates R1, R2, R3, and I3 files while bcl-convert creates R1, I1, R2, I2 files. [default: cellranger]
• -d, --outdir DIRECTORY: Directory to save files to. If none is give, save in the directory from which the script was called.
• -c, --cores INTEGER: Number of cores to use for parallel processing. [default: 18]
• -r, --rc-R2 / -R, --no-rc-R2: Should the reverse complement of R2 be used? Pass '--rc-R2' if the reads were generated on a NextSeq or v1.0 chemistry NovaSeq. [default: no-rc-R2]
• -j, --conjugation [TotalSeqA|TotalSeqB]: String specifying antibody conjugation; either TotalSeqA or TotalSeqB [default: TotalSeqA]
• --debug: Print extra information for debugging.
• --save_log: Save the log to a file
• --version: Print version number.
• --help: Show this message and exit.

Example usage:

Assuming we have FASTQs from bcl-convert in the folder /path/to/fastq/folder/sample_1 that are named:

• sample_1_prot_S11_L004_R1_001.fastq.gz
• sample_1_prot_S11_L004_R2_001.fastq.gz
• sample_1_prot_S11_L004_I1_001.fastq.gz
• sample_1_prot_S11_L004_I2_001.fastq.gz

asap-o-matic \
    --fastqs /path/to/fastq/folder \
    --sample sample_1_prot \
    --id sample_1_reformatted \
    --conjugation TotalSeqB \
    --outdir /path/to/output/sample_1 \
    --cores 24 \
    --no-rc-R2

The resulting reformatted reads will be output as:

• /path/to/output/sample_1/sample_1_reformatted_R1.fastq.gz
• /path/to/output/sample_1/sample_1_reformatted_R2.fastq.gz