Output files

<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

<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

<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

<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

<sampleName>.report.json

JSON containing summary metrics generated for a sample

<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

<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