- bins the sequenced pacbiohifi reads for visualization
- this should be used to see your sequencing runs distribution.
- also takes the bam file convert them to the fastq and estimates and plots the visualization.
- BAM support added, it converts the BAM file, reads the fastq and also puts the fasta for sending to the user.
- Make sure that the BAM and the .pbi files are in the same folder and it will read all the BAM files for the run as a regular expression.
- it uses Pterm to directly give you the visualization plots.
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/golang-pacbiohifi-visualization ±main⚡ » \
go run main.go -h
This pacbiohifi application provides the binning intervals of the sequence classification from the sequencing reads
Usage:
flag [command]
Available Commands:
bam
completion Generate the autocompletion script for the specified shell
fastq
help Help about any command
Flags:
-h, --help help for flag
Use "flag [command] --help" for more information about a command.
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/golang-pacbiohifi-visualization ±main⚡ » \
go run main.go fastq -h
Analyzes the fastq files
Usage:
flag fastq [flags]
Flags:
-h, --help help for fastq
-i, --inputfile string pacbiohifi reads file (default "inputfile for the fastq reads")
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/golang-pacbiohifi-visualization ±main⚡ » \
go run main.go bam -h
Analyzes the bam files
Usage:
flag bam [flags]
Flags:
-b, --bamfile string pacbiohifi bam file or the folder containing the bam files along with the pbi files (default "inputfile should be bam")
-h, --help help for bam
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/golang-pacbiohifi-visualization ±main⚡ » \
go run main.go fastq -i ./sample-files/samplepacbiohifi.fastq
Gaurav Sablok