https://github.com/applicativesystem/go-pacbiohifi
profiling pacbiokmers and filtering pacbio kmers
https://github.com/applicativesystem/go-pacbiohifi
bioinformatics golang golang-library pacbio-data pacbio-hifi-sequencing-reads pacbio-sequencing pacbiohifi
Last synced: 7 months ago
JSON representation
profiling pacbiokmers and filtering pacbio kmers
- Host: GitHub
- URL: https://github.com/applicativesystem/go-pacbiohifi
- Owner: applicativesystem
- License: mit
- Created: 2024-08-17T04:47:56.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-09-25T09:39:41.000Z (about 1 year ago)
- Last Synced: 2025-01-11T12:57:10.632Z (9 months ago)
- Topics: bioinformatics, golang, golang-library, pacbio-data, pacbio-hifi-sequencing-reads, pacbio-sequencing, pacbiohifi
- Language: Go
- Homepage:
- Size: 2.88 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# go-pacbiohifi
- Profiling of the pacbiohifi reads, making mers and selective filtering of the mers based on composition for better sort and filtering of the kmers and hapmers.
- Running from the binary
```
[gauravsablok@ultramarine]~/Desktop/codecreatede/golang/go-pacbiohifi% \
./go-pacbiohifi -h
This is a pacbiohifi streamline reader, which will tell you about how your sequencing pacbiohifi looks.
You can give the reads from the fastq or you can give the pacbio bam file from the sequencing
Usage:
flags [flags]
Flags:
-h, --help help for flags
-i, --inputfile string inputfile path to be given (default "path to the inputfile")
-k, --kmer int kmer to be used for the analysis (default 4)
-d, --kmerremove float kmer with this compositon to be removed (default 0.3)
-o, --ouputfile string outputfile to be given (default "path to the outputfile")
```
- Running from the github repository
```
[gauravsablok@ultramarine]~/Desktop/codecreatede/golang/go-pacbiohifi% \
go run main.go -i ./sample-files/samplepacbiohifi.fastq -k 5 -d 0.5
```
Gaurav Sablok