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  • DRAGEN Microbial Amplicon
    • ▶️DRAGEN Microbial Amplicon App Documentation
      • 🌀How to start
      • Page
      • 🧬Custom reference
        • 📄Reference BED file format
        • 📄PCR Primer definition file formats
      • 📂Output files
      • 📖Understanding the BaseSpace Reports
        • 📄Summary
        • 📄Sample Report
      • 💠Pipeline Logic
      • ⭐Special considerations for amplicon detection
      • ❓Frequently Asked Questions (FAQ)
  • DRAGEN Targeted Microbial
    • ▶️DRAGEN Targeted Microbial App Documentation
      • 🌀How to set up and run an analysis
      • 🧬Custom genomes and primer sets
        • 📄Genome definition file formats
        • 📄Primer definition file formats
      • ⚙️App Settings
      • 📖Understanding the BaseSpace Reports
        • 📄Summary Report
        • 📄Result Reports
      • 📂Output files
      • 💠Pipeline Logic
      • ⭐Special considerations for amplicon sequencing with IMAP protocols
      • ❓Frequently Asked Questions (FAQ)
      • 🚩Known issues
  • DRAGEN Microbial Enrichment Plus
    • ▶️DRAGEN Microbial Enrichment Plus App Documentation
      • 🌀How to set up and run an analysis
        • 🧬Custom reference FASTA and BED files
        • 📄Microorganism Reporting File format
      • 📂Output files
        • 📖Understanding the BaseSpace HTML reports
        • 📖Report JSON format
      • 💠Pipeline logic
      • ⭐Test information
        • 📄RPIP
        • 📄UPIP
        • 📄RVOP/RVEK
        • 📄VSP
        • 📄VSP V2
        • 📄Custom Panel
      • 🕵️‍♀️Scientific evidence
      • ❓Frequently Asked Questions (FAQ)
      • 🚩Release notes
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  • Analysis level
  • Sample level
  • amplicon/
  • consensus/
  • contig/
  • map_align/
  • metrics/
  • nextclade/
  • pangolin/
  • variant_calling/

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  1. DRAGEN Microbial Amplicon
  2. DRAGEN Microbial Amplicon App Documentation

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.

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

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Last updated 6 months ago

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