Output artifacts reference (canonical)

This page is the single source of truth for what MicroSeq writes, where it appears, and why it matters.

Use this table first, then follow the linked docs for mode-specific details.

Artifact table (seeded from paired single-run layout)

Artifact path/pattern Produced by (stage/command) What you get Why it matters
raw_ab1/*.ab1 Ingest (AB1 input retention) Copied/symlinked original chromatograms. Provenance and re-analysis from original traces.
raw_fastq/*.fastq AB1 -> FASTQ conversion Base-called FASTQ before quality trimming. Auditable conversion boundary between vendor traces and QC.
passed_qc_fastq/*.fastq Quality trimming/QC Reads passing configured QC thresholds (for example avg Q). Defines which reads are eligible for downstream assembly/BLAST.
failed_qc_fastq/*.fastq Quality trimming/QC Reads failing QC thresholds. Explains data loss and supports troubleshooting threshold choices.
qc/*_avg_qual.txt Per-read QC stats Per-file average quality/length summaries. Quick spot-check of individual read quality.
qc/trim_summary.tsv QC aggregation Combined quality/length metrics and primer-trim telemetry. Primary run-level QC report used for auditing and filtering decisions.
qc/trimmed.fasta QC output FASTA FASTA of QC-passed reads inside qc/. QC provenance copy used to verify what left trimming.
reads.fasta QC handoff Canonical merged FASTA for downstream assembly/BLAST. Stable handoff artifact so later stages use one expected input name.
qc/pairing_report.tsv Paired detection Forward/reverse pairing decisions, wells, detector signals, missing mates. Deterministic pairing audit trail in paired mode.
qc/paired_fasta/*.fasta(.qual) Paired preprocessing Direction-resolved FASTA/QUAL after trimming. Inputs used to build per-sample paired assembly inputs.
qc/paired_fasta_pretrim/*.fasta(.qual) Optional paired pretrim capture Paired FASTA/QUAL snapshots before downstream pairing/assembly steps. Debug aid for diagnosing trim-vs-pair effects.
qc/overlap_audit.tsv Overlap diagnostics (enabled paths) Candidate overlap decisions and gating outcomes. Shows why merges succeed/fail for specific samples.
qc/overlap_audit_engines.tsv Compare assemblers/engine audit Per-engine overlap diagnostics (ungapped/biopython/edlib, etc.). Explains backend differences in structural outcomes.
qc/review_queue.tsv Resolution funnel Samples queued for manual review + reasons/warnings. Focuses analyst effort on actionable ambiguity/safety cases.
asm/<sample>/<sample>_paired.fasta Paired assembly prep Per-sample concatenated paired FASTA fed to assembler. Exact per-sample sequence input entering assembly.
asm/<sample>/<sample>_paired.fasta.qual Paired assembly prep QUAL companion file for CAP3 scoring. Preserves quality-aware assembly behavior.
asm/<sample>/*.cap.contigs CAP3 assembly Assembled contigs. Main structural consensus output when overlaps are accepted.
asm/<sample>/*.cap.singlets CAP3 assembly Unassembled singlet sequences. Captures residual reads when contig assembly is partial/absent.
asm/<sample>/*.cap.info CAP3 assembly metadata CAP3 summary details (clipping/overlap stats). Primary diagnostic for CAP3 acceptance/removal behavior.
asm/assembly_summary.tsv Assembly aggregation Per-sample assembly status plus synchronized resolution fields. High-level per-sample status table for reporting and troubleshooting.
asm/blast_inputs.fasta Assembly -> BLAST handoff Final sequence sent to BLAST (contigs/singlets by policy). Defines exactly what was queried downstream.
asm/blast_inputs.tsv Assembly -> BLAST manifest Manifest of sequence-output selection, reasons, IDs, hypothesis/source mapping. End-to-end provenance from structures to BLAST input sequence IDs.
asm/compare_assemblers.tsv Compare mode Cross-backend comparison summary for selected assemblers/profiles. Supports backend/profile selection with explicit evidence.
asm/compare/<backend_or_profile>/<sample>/* Compare mode per-backend outputs Backend/profile-specific sequence outputs, merge reports, captured stdout/stderr. Deep debugging of why one assembler/profile was selected or rejected.
asm/selection_trace/*.selection_trace.tsv Compare + selector trace Structured decision trace for backend/profile selection. Reproducible explanation of automated selection decisions.
hits.tsv microseq blast Raw BLAST hits table. Core homology evidence before taxonomy joins.
hits_tax.tsv microseq add-taxonomy BLAST hits with taxonomy columns appended. Interpretable taxonomic output for downstream summarization.
results.biom (or chosen BIOM output) microseq postblast BIOM table aligned with metadata/taxonomy. Direct handoff to QIIME2/phyloseq/scikit-bio ecosystems.
<output>_blast_provenance.csv microseq postblast sidecar BLAST provenance table alongside BIOM output. Transparency for post-BIOM record lineage and joins.
<output>_taxonomy_only.csv microseq postblast sidecar Taxonomy-focused export. Lightweight table for taxonomy-only checks and reporting.
<output>_metadata.csv microseq postblast sidecar Metadata-aligned output table. Verifies metadata join behavior and sample-ID normalization effects.

Abbreviated paired single-run tree (reference layout)

paired_single_pair_ab1_demo_run_microseq/
├── raw_ab1/
├── raw_fastq/
├── passed_qc_fastq/
├── failed_qc_fastq/
├── qc/
│   ├── trim_summary.tsv
│   ├── pairing_report.tsv
│   ├── overlap_audit.tsv
│   ├── review_queue.tsv
│   └── trimmed.fasta
├── reads.fasta
├── asm/
│   ├── assembly_summary.tsv
│   ├── blast_inputs.fasta
│   ├── blast_inputs.tsv
│   ├── compare_assemblers.tsv
│   ├── compare/
│   └── selection_trace/
├── hits.tsv
└── hits_tax.tsv