inrb-labgenpath/singa-illumina

## 🌿 MpxV-SINGA : 🦠 MonkeyPox Virus - 🧬 Sequence Information from 🧪 Nucleotide Generation and 🛠️ Assembly %20%7C%20Catalina%20(10.15.7)%20%7C%20Big%20Sure%20(11.6.3)%20%7C%20Monterey%20(12.6.0)%20%7C%20Ventura%20(13.3.1)%20%7C%20Sonoma(%2014.2.1)/E6055C?icon=apple&label&list=%7C&scale=0.9) %20%7C%20Focal%20Fossa%20(20.04)%20%7C%20Jammy%20Jellyfish%20(22.04)/772953?icon=svgrepo.com) %20%7C%20Focal%20Fossa%20(20.04)%20%7C%20Jammy%20Jellyfish%20(22.04)/00BCF2?icon=windows&label&list=%7C&scale=0.9) ## Introduction `SINGA` is a bioinformatics analysis pipeline designed for the assembly and variant calling of Monkeypox Virus (MPXV) samples. This pipeline places an emphasis on quality control, ensuring that low-quality reads are filtered out, primers are effectively trimmed, and human-derived reads are depleted. As a result, users can obtain high-quality MPXV sequences. Tailored specifically for Illumina sequencing data (singa-illumina repository), SINGA is optimized for amplicon-based approaches, focusing on data generated using carefully curated primer sets. ## Pipeline Overview `SINGA` is designed with flexibility in mind, enabling users to execute specific components of the workflow as needed. For example, users can create an environment.yml file to manage dependencies using Conda, ensuring a reproducible environment for their analyses. The pipeline effectively integrates both Bash and Python scripts, all of which are managed by the Snakemake workflow manager. Furthermore, users have full access to all pipeline files, allowing them to edit and customize the workflow according to their specific requirements. -------------------------------------------------------------------------------------------------------------------------------------------------------------- : Visualize reads quality before and after the reads trimming : Remove adapters and low quality reads …