README.md

FORK: cellatlas

This is a fork of the source cellatlas with a view to updating to work with the latest version of seqspec.

Hackathon

Notes for hackathon here.

Universal preprocessing of single-cell genomics data

The cellatlas tool uses seqspec and kallisto bustools to facilitate universal preprocessing of single-cell genomics data.

Installation

The cellatlas command-line tool can be installed with pip:

pip install git+https://github.com/cellatlas/cellatlas.git

and can be run with

cellatlas build \
-o out \
-m modality \
-s spec.yaml \
-fa http://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz \
-g http://ftp.ensembl.org/pub/release-109/gtf/homo_sapiens/Homo_sapiens.GRCh38.109.gtf.gz \
-fb feature_barcodes.txt \
fastqs/R1.fastq.gz fastqs/R2.fastq.gz",

• -o is the output folder
• -m is the modality (rna/atac etc)
• -s is the seqspec for the supplied FASTQs
• -fa is either a link to the genome FASTA or the file itself
• -g is either a link to the genome annotation (GTF) or the file itself
• -fb is optional and is the feature barcode file for tag/protein/crispr assays

FASTQs are supplied at the end of the command in any order.