single-nucleus utility in python
Git clone or download this repository, then change the path in the config file before running snakemake.
snuupy.py [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Commands:
addGeneName parse polished reads mapping results and
get...
addPolyATag add polyA length tag for bam files
addUnmappedBaseTag get unmapped base tag
barcodeAssignment assign barcode for each Nanopore read;
based...
generateH5adFromKb get adata from kbpython result --tg:...
generateIlluminaWindow output illumina reads based on mapping info
generateIlluminaWindowFromKb generate illumina windows from kb_python...
generateMtx generate matrices
generateNanoporeWindow output nanopore reads based on mapping info
getMismatch calculate mismatch based on blast results
getSpliceInfo get splice information which used for...
multilayerClustering cluster nuclei by snf or mofa
parseIllumina parse Illumina bam file and generate...
polishReads polish barcode assigned Nanopore reads
polyAClusterDetected detect PolyA Cluster
windowBlast blast find potential UMI/Bc
- python3
- pandas
- scipy
- numpy
- scanpy
- joblib
- loguru
- portion
- ont-fast5-api
- more_itertools
- biopython
- pyfastx
- snfpy
- mofapy2
- abPOA
- tqdm
- pysam
- portion
- R
- scran
- Snakemake
- minimap2
- seqkit
- racon
- picard
This pipeline was inspired by Sicelore
Function multilayerClustering is inspired by scLAPA