https://github.com/applicativesystem/go-alignment-merger

a goroutines implementation for clipping off the genome alignment and making genome structs
https://github.com/applicativesystem/go-alignment-merger

bioinformatics genome-analysis genome-phylogenomics goroutine phylogenomics phylogenomics-golang

Last synced: 7 days ago
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a goroutines implementation for clipping off the genome alignment and making genome structs

• Host: GitHub
• URL: https://github.com/applicativesystem/go-alignment-merger
• Owner: applicativesystem
• License: mit
• Created: 2024-09-16T19:25:38.000Z (3 months ago)
• Default Branch: main
• Last Pushed: 2024-09-29T07:48:22.000Z (3 months ago)
• Last Synced: 2024-11-10T20:18:08.684Z (about 1 month ago)
• Topics: bioinformatics, genome-analysis, genome-phylogenomics, goroutine, phylogenomics, phylogenomics-golang
• Language: Go
• Homepage:
• Size: 14.6 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# goroutines-alignment-merger

- large scale alignment merger for phylogenomics.

- a large phylogenomics datasets merged in less than few minutes for the genome scale alignment.

- check the alignment-go package which has all alignment utilities.

```

# run this on the fasta if your alignment fasta are NCBI formatted to make it linearized.

awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  \

                         END {printf("\n");}' fastafile > alignment.go.fasta

go run main.go

  -alignmentfile string

        file (default "path to the alignment file")

  -title string

        gene name (default "name of the header of the gene")

[gauravsablok@fedora]~/Desktop/codecreatede/goroutines-alignment-clipper% \

      go run main.go -alignmentfile ./sample-files/alignment.go.fasta -title merged

> merged

ATG.....

a large phylogenomics datasets merged in less than few minutes for the genome scale alignment. 

```

Gaurav Sablok