📂Output files

Note: Some files may not be generated depending on user inputs and pipeline outcome

Analysis level

• Analysis_Results/<analysisId>.report.html displays tables and plots that summarize results from all samples combined.

• Analysis_Results/all_consensus.fasta contains all consensus sequences generated in the analysis. This is generated by concatenating <sampleName>.sample_consensus.fasta from all samples.

Sample level

An output directory named after each sample contains <sampleName>.html, which displays tables and plots specific to the sample. The HTML files are identical to the ones displayed in BaseSpace Reports.

Each sample directory also contains the following subdirectories and output files:

amplicon/

<sampleName>.amplicon_coverage.log	Log from computing coverage metrics for each amplicon in a sample
<sampleName>.amplicon_coverage.csv	CSV reporting coverage metrics for each amplicon in a sample
<sampleName>.amplicon_detection.json	JSON reporting amplicon detection results for a sample

consensus/

<sampleName>.hard_masked_consensus.fa	FASTA containing all hard-masked consensus sequences generated for a sample
<sampleName>.soft_masked_consensus.fa	FASTA containing all soft-masked consensus sequences generated for a sample
<sampleName>.sample_consensus.fasta	<sampleName>.hard_masked_consensus.fa but with informative headers
<sampleName>_<genomeName>.genome_consensus.fasta	<sampleName>.sample_consensus.fasta but specific to consensus sequences generated using reference sequences that belong a particular genome
<sampleName>_<accessionName>.accession_consensus.fasta	<sampleName>.sample_consensus.fasta but specific to consensus sequences generated using a particular reference sequence
<sampleName>.consensus.json	JSON containing information on all consensus sequences generated for a sample

contig/

<sampleName>.sample_contig.fasta	FASTA containing all contig sequences generated for a sample
<sampleName>_<genomeName>.genome_contig.fasta	<sampleName>.sample_contig.fasta but specific to contigs mapping to reference sequences that belong a particular genome
<sampleName>_<accessionName>.accession_contig.fasta	<sampleName>.sample_contig.fasta but specific to contigs mapping to a particular reference sequence
<sampleName>.contig.json	JSON containing information on all contig sequences generated for a sample

map_align/

<sampleName>-replay.json	JSON reporting parameters and versions used when running DRAGEN to perform short read alignment
<sampleName>-unmapped_ S1_L001_R1_001.fastq.gz	FASTQ containing R1 reads that did not map to any selected reference sequences
<sampleName>-unmapped_ S1_L001_R2_001.fastq.gz	FASTQ containing R2 reads that did not map to any selected reference sequences
<sampleName>-unmapped-singleton_S1_L001_R1_001.fastq.gz	FASTQ containing singleton reads that did not map to any selected reference sequences
<sampleName>.bam	BAM containing all short read alignments
<sampleName>.bam.bai	BAI for <sampleName>.bam
<sampleName>.mapping_metrics.csv	CSV generated by DRAGEN to report mapping metrics
<sampleName>.trim.log	Log from performing post-facto primer trimming after short read alignment
<sampleName>.trimmer_metrics.csv	CSV generated by DRAGEN to report trimmer metrics
dragen_run_<runId>.log	Log from running DRAGEN to perform short read alignment

metrics/

<sampleName>.coverage.tsv	TSV reporting base-pair resolution coverage values across all reference sequences used in short read alignment
<sampleName>.report.json	JSON containing summary metrics generated for a sample

nextclade/

<sampleName>_<datasetName>.aligned.fasta	FASTA generated by Nextclade from aligning consensus sequences to a reference sequence
<sampleName>_<datasetName>.auspice.json	Auspice JSON generated by Nextclade containing output phylogenetic tree
<sampleName>_<datasetName>.csv	CSV generated by Nextclade to report results from mutation calling, clade assignment, quality control, etc.
<sampleName>_<datasetName>.json	<sampleName>_<datasetName>.csv in JSON format
<sampleName>_<datasetName>.ndjson	<sampleName>_<datasetName>.csv in NDJSON format
<sampleName>_<datasetName>.tsv	<sampleName>_<datasetName>.csv in TSV format

pangolin/

variant_calling/

<sampleName>-replay.json	JSON reporting parameters and versions used when running DRAGEN to perform variant calling
<sampleName>.consensus_filtered.bcftools_stats.txt	TXT generated by BCFtools stats command to report statistics on called variants that passed the consensus filter
<sampleName>.consensus_filtered.summary.csv	CSV generated by BCFtools query command to summarize called variants that passed the consensus filter
<sampleName>.consensus_filtered.vcf.gz	VCF containing called variants that passed the consensus filter
<sampleName>.consensus_filtered.vcf.gz.tbi	TBI for <sampleName>.consensus_filtered.vcf.gz
<sampleName>.hard-filtered.bcftools_stats.txt	TXT generated by BCFtools stats command to report statistics on called variants
<sampleName>.hard-filtered.summary.csv	CSV generated by BCFtools query command to summarize called variants
<sampleName>.hard-filtered.vcf.gz	VCF containing called variants
<sampleName>.hard-filtered.vcf.gz.tbi	TBI for <sampleName>.hard-filtered.vcf.gz
<sampleName>.vc_metrics.csv	CSV generated by DRAGEN to report variant calling metrics
dragen_run_<runId>.log	Log from running DRAGEN to perform variant calling