This directory contains the complete workflow scripts for assembling and annotating the LSL-SFB (chicken Segmented Filamentous Bacteria) genome.
The pipeline consists of 7 main steps:
- BWA Alignment - Align HiC reads to chicken genome + turkey SFB reference
- Extract SFB Reads - Extract reads mapping to turkey SFB contigs
- Generate Consensus - Create consensus sequence using samtools
- POLCA Polishing - Polish consensus with POLCA
- HiC Scaffolding - Scaffold with Juicer and 3D-DNA
- Prokka Annotation - Annotate genome with Prokka
- Quality Assessment - Assess quality with BUSCO and CheckM
- 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