A tool to extract barcode and UMI from Nanopore(Oxford Nanopore Technologies) reads.
Full length read
5' - read1(adapter) - bc1 - linker1 - bc2 - linker2 - bc3 - C - UMI - polyT - insert - TSO
- Locate the polyT(or polyA if the read is on the reverse strand) region in the read. Reverse complement the read if it is on the reverse strand.
- Discard all the read that is considered as a fused read(contain multiple polyT).
- Extract cell barcodes and UMIs by using (adapter,linker,polyT) as anchor.
- Barcode correction.
pip install celescope editdistance
It also needs libssw.so from SSW Library
gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h
Then put libssw.so under the same directory of ONT_extract.py
usage: ONT_extract.py [-h] [-c CELLBC] [--only_cell] fastq
positional arguments:
fastq fastq file
optional arguments:
-h, --help show this help message and exit
-c CELLBC, --cellBC CELLBC
The path of barcodes.tsv file from short-reads library. If provided, the cell barcodes from short reads
libary will be used to calculate fraction of reads in cells.
--only_cell Only output reads in cells. Use together with --cellBC.
bc_umi.fa: fasta file of barcodes and UMIs seperated by ':'
>216dc340-3abe-442a-8ac6-d2fac2fb1ff9 88
ATCGACACG_TCTGTCTGC_TGACAGCTA:ATGGCAAGTACT
>fe4f515a-90ea-4ff1-aed4-4ed96ba9f06a 91
GAGCAGCTT_ATAGCGTGT_ACTCGGATT:GAAGTTTTGTTT
>8c84c4a6-787b-4fb5-981f-d86a7aa712c2 84
CGCAACTAC_CCTACAAGG_GAAGCCATT:CCCCGCCAAGTT
>099fae10-de27-4e58-ab70-430c3860db69 88
insert.fq: fastq file of the insert sequences. Sequences before the polyT are trimmed.