Usage: cd TelFinder-main/
Q:check the parameters and its meanings python3 TelFinder.py -h
Q:format=fasta python3 TelFinder.py -f fa -inf example/fasta/NCR.fna -s NCR -o example/fasta -e left python3 TelFinder.py -f fa -inf example/fasta/NCR.fna -s NCR -o example/fasta -e right
Q:format=fastq(single) python3 TelFinder.py -f fq1 -inf example/fastq/DD.fastq -ref example/fastq/AFM_genomic.fna -o example/fastq/ -s AFMfq -t 80
Q:format=fastq(paired) python3 TelFinder.py -f fq2 -1 example/fastq/DRR237583_1.fastq -2 example/fastq/DRR237583_2.fastaq -ref example/fastq/AFM_genomic.fna -o example/fastq/ -s AFMfq -t 80
Q:varaition analysis, format=kmer_fa python3 TelFinder.py -f kmer_fa -inf example/fasta/NCR.fna -m CCCTAA -o example/fasta/ -s NCR -e left
Q:varaition analysis, format=kmer_fq1 python3 TelFinder.py -f kmer_fq1 -inf example/fastq/DD.fastq -ref example/fastq/AFM_genomic.fna -m CCCTAA -o example/fasta/ -s AFMfq -e left
Q:varaition analysis, format=kmer_fq2 python3 TelFinder.py -f kmer_fq2 -1 example/fastq/DRR237583_1.fastq -2 example/fastq/DRR237583_2.fastq -ref example/fastq/AFM_genomic.fna -m CCCTAA -o example/fasta/ -s AFMfq -e left
If you use the TelFinder in a publication or web page, please cite the following paper: Sun, Q., Wang, H., Tao, S., & Xi, X. (2023). Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder. Microbiology spectrum, 11(2), e0392822. Advance online publication. https://doi.org/10.1128/spectrum.03928-22