LSL-SFB Genome Assembly Pipeline Scripts

This directory contains the complete workflow scripts for assembling and annotating the LSL-SFB (chicken Segmented Filamentous Bacteria) genome.

Workflow Overview

The pipeline consists of 7 main steps:

1. BWA Alignment - Align HiC reads to chicken genome + turkey SFB reference
2. Extract SFB Reads - Extract reads mapping to turkey SFB contigs
3. Generate Consensus - Create consensus sequence using samtools
4. POLCA Polishing - Polish consensus with POLCA
5. HiC Scaffolding - Scaffold with Juicer and 3D-DNA
6. Prokka Annotation - Annotate genome with Prokka
7. Quality Assessment - Assess quality with BUSCO and CheckM

Software Requirements

• BWA v0.7.17
• SAMtools v1.19.1
• MaSuRCA (for POLCA)
• Juicer v1.5.7
• 3D-DNA v180114
• JuiceBox v1.11 (for manual curation)
• Prokka v1.14.6
• BUSCO v5.x
• CheckM