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https://github.com/applicativesystem/go-pacbiohifi-visualization
streaming visualization of pacbiohifi reads
https://github.com/applicativesystem/go-pacbiohifi-visualization
bioinformatics genome-analysis genome-informatics pacbio-hifi-sequencing-reads pacbio-sequencing
Last synced: 19 days ago
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streaming visualization of pacbiohifi reads
- Host: GitHub
- URL: https://github.com/applicativesystem/go-pacbiohifi-visualization
- Owner: applicativesystem
- License: mit
- Created: 2024-09-24T18:39:36.000Z (3 months ago)
- Default Branch: main
- Last Pushed: 2024-10-05T21:30:03.000Z (3 months ago)
- Last Synced: 2024-11-10T20:18:10.542Z (about 2 months ago)
- Topics: bioinformatics, genome-analysis, genome-informatics, pacbio-hifi-sequencing-reads, pacbio-sequencing
- Language: Go
- Homepage:
- Size: 6.98 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# go-pacbiohifi-visualization
- 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](https://github.com/pterm/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 readsUsage:
flag [command]Available Commands:
bam
completion Generate the autocompletion script for the specified shell
fastq
help Help about any commandFlags:
-h, --help help for flagUse "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 filesUsage:
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 filesUsage:
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```
![](https://github.com/codecreatede/go-pacbiohifi-visualization/blob/main/go-pacbiohifivisualization.png)
Gaurav Sablok