Environment and wrapper scripts for bases2fastq to demultiplex sequencing output from the AVITI sequencer.

Directory

• conda_bases2fastq/: conda environment created by conda env update -f bases2fastq.yml --prune (use same command to update the environment if bases2fastq.yml is updated). This contains the Python packages required by bases2fastq to generate QC reports, as described in the bases2fastq documentation: https://docs.elembio.io/docs/bases2fastq/setup/.
• bases2fastq: symbolic link to the latest bases2fastq binary.
• bases2fastq-#.#.#: bases2fastq binaries, with their version numbers indicated.
• bases2fastq.sbatch: SLURM batch script submitted by demultiplex.sh. When run, activates the conda environment in conda_bases2fastq/ and runs bases2fastq.
• bases2fastq.yml: specifies the conda environment installed in conda_bases2fastq/.
• demultiplex.sh: Main wrapper script run by the user to generate demultiplexed FASTQ files from an AVITI sequencing run. Run it without arguments for a help message. Provides default values for the --num-threads (8) and --filter-mask ('R1:N*-R2:N*') arguments of bases2fastq.

Contributors

• Benjamin Yeh (@bentyeh)