https://github.com/applicativesystem/go-multi-longread-canvas
multipattern trimmomatic for long reads
https://github.com/applicativesystem/go-multi-longread-canvas
bioinformatics bioinformatics-algorithms genome-sequencing nanopore-sequencing pacbio-hifi-sequencing-reads pacbio-sequencing
Last synced: about 2 months ago
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multipattern trimmomatic for long reads
- Host: GitHub
- URL: https://github.com/applicativesystem/go-multi-longread-canvas
- Owner: applicativesystem
- Created: 2024-10-28T22:23:27.000Z (7 months ago)
- Default Branch: main
- Last Pushed: 2024-10-28T22:33:43.000Z (7 months ago)
- Last Synced: 2024-12-16T02:12:08.515Z (5 months ago)
- Topics: bioinformatics, bioinformatics-algorithms, genome-sequencing, nanopore-sequencing, pacbio-hifi-sequencing-reads, pacbio-sequencing
- Language: Go
- Homepage:
- Size: 2.81 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# go-multi-longread-canvas
- multi-trimmomatic for the long reads, no heap memory allocation required, runs on goroutines and later adding the waitgroup.
- in this version, it supports the multiple patterns as in the last release of trimmomatic.
- parsed 100GB fastq file in few seconds.
- check the multipattern file for how to define the pattern.
```
╭─gauavsablok@gauravsablok ~/Desktop/go/go--multi-longread-canvas ‹main●›
╰─$ go run main.go -h
look for the matching patterns
Usage:
longread [flags]
Flags:
-h, --help help for longread
-L, --longread string long read file to be checked (default "path to the long read file")
-P, --pattern string pattern file (default "path to the file containing the patterns")
exit status 1
```
-detailed usage
```
╭─gauavsablok@gauravsablok ~/Desktop/go/go-multi-longread-canvas ‹main●›
╰─$ go run main.go -L sample.fastq -P pattern.txt
The canavssed reads have been written
exit status 1
╭─gauavsablok@gauravsablok ~/Desktop/go/go-multi-longread-canvas ‹main●›
╰─$ cat sample.fastq
@ERR10930361.1 magdelm64071_201030_115446/27
ATACTTTAAATTTTAGTTACTATTATTATTATTTAAAAAAAAAAAAAAAATTGAAAGTATATCCAAACTA
@ERR10930361.1 magdelm64071_201030_115446/27
ATACTTTAAATTTTAGTTACTATTATTATTATTTAAAAAAAAAAAAAAAATTGAAAGTATATCCAAACTAGCACTCAATTAATGCAAACAAT
╭─gauavsablok@gauravsablok ~/Desktop/go/go-multi-longread-canvas ‹main●›
╰─$ cat canvased.fastq
@ERR10930361.1
ATACTTTAAATTTTAGTTACTATTATTATTATTTTTTCCAAACTA
@ERR10930361.1
ATACTTTAAATTTTAGTTACTATTATTATTATTTTTTCCAAACTAGCACTCAATTAATGCAAACAAT
```
Gaurav Sablok