bases2fastq-nf is a bioinformatics pipeline used to demultiplex the raw data produced by the Element AVITI™ System using the Bases2Fastq Software. Bases2Fastq processes sequencing data and converts base calls into FASTQ files. During a sequencing run, the Element AVITI™ System records base calls and associated quality scores (Q-scores) in bases files. Bases2Fastq converts the bases files into the FASTQ file format for secondary analysis with the FASTQ-compatible software of your choice.

• The Bases2Fastq Documentation has detailed execution information for changing parameters.
• The Run Manifest Documentation has detailed information for resetting demultiplexing settings, controlled by the input Run Manifest.

Bases2fastq-nf enables you to run Bases2Fastq on any environment that supports running nextflow.

nextflow run commands

nextflow run . -profile test
nextflow run . -profile test_index_fastq
nextflow run . -profile test_legacy_fastq
nextflow run . -profile test_projects
nextflow run . -profile test_qc_only
nextflow run . -profile test_custom_manifest_s3
nextflow run . -profile test_custom_manifest_local
nextflow run . -profile test_custom_manifest_rundir
nextflow run . -profile test_s3
nextflow run . -profile test_s3_zipped

Run nf-test

nf-test test

License

Use subject to license available at go.elembio.link/eula.