A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi, quick question. Have someone used airrflow pipeline for Smart-seq data or other well-based single-cell sequencing? We are doing a test from from a non-targetted gene expression library to see if we can get heavy and light chain paired up.

I not doing it for human and mouse data either, so I need to be able to input a custom database.

w.r.t. single cell:
airrflow can run the process from fastq files if the data comes from 10x genomics.
Otherwise you can give AIRR-seq files as input for airrflow

I see, so it won't separate each cell based on their barcode if it is not 10x.

yes, for sc sequence alignment it currently only supports 10x