https://github.com/applicativesystem/go-diamond-tags
metacoverage estimation and tags generation from diamond aligner
https://github.com/applicativesystem/go-diamond-tags
genome-analysis genome-analysis-annotation genome-annotation metagenome-annotation metagenome-assembled-genomes metagenome-assembly
Last synced: 6 months ago
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metacoverage estimation and tags generation from diamond aligner
- Host: GitHub
- URL: https://github.com/applicativesystem/go-diamond-tags
- Owner: applicativesystem
- License: mit
- Created: 2024-10-03T10:44:36.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-10-16T05:36:51.000Z (12 months ago)
- Last Synced: 2024-12-16T02:12:08.757Z (10 months ago)
- Topics: genome-analysis, genome-analysis-annotation, genome-annotation, metagenome-annotation, metagenome-assembled-genomes, metagenome-assembly
- Language: Go
- Homepage:
- Size: 5.65 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# go-diamond-tags
- a subfunction for the diamond-aligner and estimating the hsp coverage
- this is also integratd into the go-mapper-diamond
- you can use this as a separate if you have already aligned reads to the protein.
- when you have a metagenome and you want to generate the annotation tags using the bacterial genome proteins.
- when you have MAGS and you want to generate the specific mags to protein alignment.
- same goes for other species also.
- your pacbio reads should be a linear fasta, which is the way the pacbio reads usually comes.
- Incase of the other fasta sequences such as genomes or others, remember to run the awk utility to linearize it. This is faster than implementing a loop iteration.
```
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} \
END {printf("\n");}' inputfasta > output.fasta
```
```
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-tags ±main⚡ » \
go run main.go -h
Analyzer for the diamond aligner and pacbio reads for hints
Usage:
analyze [command]
Available Commands:
alignment
completion Generate the autocompletion script for the specified shell
help Help about any command
Flags:
-h, --help help for analyze
Use "analyze [command] --help" for more information about a command.
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-tags ±main⚡ » \
go run main.go alignment -h
Analyzes the hsp from the diamond read to protein alignment
Usage:
analyze alignment [flags]
Flags:
-a, --alignmentfile string alignment (default "alignment file to be analyzed")
-h, --help help for alignment
-p, --pacbioreads string pacbio file (default "pacbio reads file")
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-tags ±main⚡ » \
go run main.go alignment -a matches.tsv -p ./samplefiles/pacbioreads.fasta
chr10:66478458-66505490 1.0061776347427218
chr10:66478458-66505490 0.9026005252839123
chr11:66478458-66505490 0.8952021603225687
chr11:66478458-66505490 1.0875596493175008
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-tags ±main⚡ » \
cat coveragestimation.txt
chr10:66478458-66505490 1.0061776347427218
chr10:66478458-66505490 0.9026005252839123
chr11:66478458-66505490 0.8952021603225687
chr11:66478458-66505490 1.0875596493175008
```
Gaurav Sablok