NanoSTR: A method for detection of targeted short tandem repeats (STRs) based on nanopore sequencing data
NanoSTR is a method for STR typing based on nanopore sequencing data and the reads’ length-number-rank (LNR) information. NanoSTR not only improves the effective use of sequencing data but also shows higher accuracy compared with the existing genotypical methods. NanoSTR provides an alternative analytical method for the detection of STR loci by nanopore sequencing and adds to the related data analysis tools. We hope that NanoSTR can further expand the application of nanopore sequencing techniques in scientific research and clinical scenarios so that these techniques can better promote the development of the sequencing industry and serve the needs of precision medicine.
Option
-fq <Raw Fastq File> Input nanopore sequencing raw data
-step_size <Step Size> Extraction times
-configure <STR BED File> STR bed file, the format likes: chr start end str_name
-tmp_dir <Tmpfile Dir> The tmpdir prefix
-process <Number of process used> N processes to use, default is 1
-help print HELP message
Example:
perl NanoStrTyping.pl -fq nanopore.fastq -step_size 10 -configure STR.bed -tmp_dir tmpdir -process 1
The STR.bed format's example:
chrY 22633873 22633911 DYS392
chrY 14937824 14937873 DYS438
chrY 24365070 24365225 DYS448
chrY 14379564 14379655 DYS635
chrY 15278737 15278851 DYS447
The method is still under further optimization and development, please contact us if you have any good suggestions and questions.
Contact and E-mail: langjidong@hotmail.com