Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/chocogangsta/belajar

https://github.com/chocogangsta/belajar

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (1.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: chocogangsta
  • Language: Shell
  • Default Branch: main
  • Size: 25.4 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme

README.txt 

In-House Bioinformatics Pipeline

Dikembangkan untuk keperluan pembelajaran analisis bioinformatika dasar

Pipeline ini disusun untuk memberikan pengalaman praktis dalam menganalisis data sekuensing, khususnya shotgun metagenomics dan Oxford Nanopore Technology (ONT).
Cocok digunakan oleh peneliti, mahasiswa, atau teknisi laboratorium yang ingin memahami alur kerja analisis bioinformatika secara menyeluruh.

  ⚠️ Catatan Penting:
      > Pipeline ini hanya ditujukan untuk keperluan pembelajaran dan bukan untuk analisis resmi atau diagnosis klinis.

🔧 Persyaratan Aplikasi
Sebelum menjalankan pipeline, pastikan Anda telah menginstal software berikut:

Aplikasi 

1. Fastp (quality control, trimming, filtering, dll)
   > https://github.com/OpenGene/fastp

2. BWA	mem (Mapping to Reference) for Illumina 
   > https://github.com/lh3/bwa

3. Minimap2 (Mapping to Reference) for Oxford Nanopore Technology / Pacbio
   > https://github.com/lh3/minimap2

4. Samtools	(Manipulate SAM/BAM File from Mapping)
   > https://github.com/samtools/samtools

5. Bcftools	(Varian calling dan manipulating VCF/BCF file) 
   > https://github.com/samtools/bcftools


🚀 Cara Menjalankan Pipeline
       > bash Installation.sh <

File >config.txt< adalah file konfigurasi utama. Anda harus menyesuaikan isinya sesuai dengan:

       1. Lokasi FastQ File        <
       2. Lokasi Reference Genome  <
       3. Lokasi bed File          <

🚀 Cara Menjalankan Pipeline
       1. For Illumina
          > bash Illumina.sh config.txt <
       2. For ONT
          > bash ONT.sh config.txt <

Owner

  • Login: chocogangsta
  • Kind: user

GitHub Events

Total
  • Push event: 9
  • Public event: 1
Last Year
  • Push event: 9
  • Public event: 1