CDPHE-RSV This repository contains in development files for a pipeline to process RSV sequence data and summarize their data. Limitations The current in dev version only takes paired-end (PE) reads. Next generation sequencing and bioinformatic and genomic analysis at CDPHE is not CLIA validated at this time. These workflows and their outputs are not to be used for diagnostic purposes and should only be used for public health action and surveillance purposes. CDPHE is not responsible for the incorrect or inappropriate use of these workflows or their results. Workflow graph TD subgraph Assembly A1(Raw Reads) --> B1 A1 --> C1 B1[filter_reads_seqyclean] --> D1 B1 --> L1 C1[assess_quality_fastqc] --> L1 D1[align_reads_bwa] --> E1 D1 --> L1 E1[trim_primers_ivar] --> F1 E1 --> G1 E1 --> H1 F1[call_variants_ivar] --> L1 G1[call_consensus_ivar] --> I1 G1 --> L1 H1[calc_bam_stats_samtools] --> L1 I1[rename_fasta] --> J1 I1 --> K1 I1 --> L1 J1[calc_percent_coverage] --> L1 K1[call_clades_nextclade] --> L1 L1([Assembly Files]) --> M1 M1[transfer_outputs] --> N1 N1{{Cloud Bucket}} end graph TD subgraph Summary A2(Assembly Files) --> B2 B2[concatenate_consensus] --> D2 A2 --> C2 C2[summarize_results] --> D2 D2([Summary Files]) --> E2 E2[transfer_outputs] --> F2 F2{{Cloud Bucket}} end