What this page is for

Use this page when you want to run MicroSeq from a terminal, inside a bash wrapper, over SSH, or on an HPC cluster. It documents the current headless paired-AB1 workflow and shows how the wrapper maps onto the underlying MicroSeq CLI stages.

This page is operational. For pairing rules, assembly semantics, ambiguity handling, and BLAST-input behavior, see the Paired CAP3 Assembly Tutorial. For the meaning of output files, see Output Artifacts Reference.

When to use this page instead of the GUI

Use the CLI/HPC workflow when:

  • you want reproducible batch runs
  • you are working on a remote server or cluster
  • you want to call MicroSeq from a shell script or scheduler
  • you want one run-scoped log across multiple stages
  • you want a stable operational workflow that mirrors the paired pipeline without relying on interactive dialogs

MicroSeq CLI / HPC Quickstart

Install MicroSeq

For installation, environment setup, and database setup, follow the main README:

  • GitHub repo: https://github.com/jose-cantu/MicroSeq
  • README: https://github.com/jose-cantu/MicroSeq/blob/master/README.MD

This includes:

  • creating and activating the MicroSeq conda environment
  • installing the package
  • running microseq-setup
  • configuring databases and logging

Once installation is complete, activate the environment:

conda activate MicroSeq

Current paired AB1 HPC workflow

For using the bash wrappers I have setup refer to this readme I made here:

  • AB1 CLI README: https://github.com/jose-cantu/MicroSeq/tree/master/workflows

The current bash wrapper for paired AB1 runs is:

bash workflows/paired_ab1_pipeline.sh <input_dir> <db_key> <blast_threads> [out_dir]

Arguments:

  • input_dir = directory containing raw paired .ab1 files
  • db_key = gg2, silva, or ncbi
  • blast_threads = number of threads to pass to BLAST
  • out_dir = optional output directory; default is <input_dir>_microseq

Minimal example

conda activate MicroSeq

bash workflows/paired_ab1_pipeline.sh \
  tests/paired_single_pair_ab1_demo_run \
  gg2 \
  4

Optional primer-label override

If your forward and reverse primer labels differ from the demo defaults, override them before running the wrapper:

conda activate MicroSeq

export FWD_PATTERN="27F"
export REV_PATTERN="1492R"

bash workflows/paired_ab1_pipeline.sh \
  /path/to/paired_ab1_inputs \
  gg2 \
  4

Optional run-scoped logging

If you want every microseq stage launched by the wrapper to write into one run-scoped log context:

export MICROSEQ_SESSION_ID="paired-run-001"

Then run the wrapper normally.

What the wrapper currently does

The wrapper currently runs the paired AB1 workflow in this order:

  1. trim AB1 -> QC-passed FASTQ
  2. stage paired FASTA/QUAL
  3. write qc/pairing_report.tsv
  4. run paired assembly
  5. write asm/assembly_summary.tsv
  6. write qc/overlap_audit.tsv
  7. write asm/blast_inputs.fasta and asm/blast_inputs.tsv
  8. run BLAST
  9. join taxonomy

Key outputs

After a successful run, the main outputs are:

  • qc/trim_summary.tsv
  • qc/pairing_report.tsv
  • qc/overlap_audit.tsv
  • asm/assembly_summary.tsv
  • asm/blast_inputs.fasta
  • asm/blast_inputs.tsv
  • hits.tsv
  • hits_tax.tsv

Notes

  • Use the README for installation and setup.
  • Use the 2nd README in /workflow for the preview pairs wrapper and this wrapper for the current headless paired AB1 workflow.
  • For pairing/assembly behavior and output semantics, see the paired assembly documentation in /docs.