MicroSeq Docs
MicroSeq is a microbiology-focused Sanger workflow for turning raw AB1 or FASTQ reads into QC-passed sequences, paired assemblies when appropriate, BLAST results, taxonomy-aware tables, and optional downstream BIOM outputs.
If you are using MicroSeq for 16S isolate identification or related microbiology workflows, this page is the best place to start.
Where should I start?
Most microbiology users
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GUI Walkthrough how to run MicroSeq through the graphical interface -
Output Artifacts Reference what files MicroSeq writes and what they mean
If you are working with paired forward/reverse Sanger reads
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Paired CAP3 Assembly Tutorial what paired mode means biologically and how MicroSeq decides what goes to BLAST -
GUI Table Reference detailed meanings of GUI table columns
If you are running from a terminal, remote server, or HPC
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CLI Workflows current headless workflow and wrapper usage
Advanced and reference pages
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Workflow Resolution Funnel advanced status routing, ambiguity handling, and sample-level evidence collapse -
MicroSeq’s Design: Questions & Answers practical design explanations -
VSEARCH Chimera & Replicate Filters optional VSEARCH-related workflows
Tiny glossary
| Term | Meaning |
|---|---|
Q-cov |
Query coverage. This is the percentage of your query sequence covered by the alignment to a database hit. |
contig |
A merged consensus sequence built from overlapping read evidence, such as forward and reverse reads from the same sample. |
singlet |
A standalone sequence record that remains usable when a defended merged contig was not produced. |
pair_missing |
A paired-mode outcome where only one direction survived pairing, so the sample never had a valid forward/reverse assembly opportunity. |
filename primer labels |
The labels in the filename, such as 27F or 1492R, that MicroSeq uses to recognize forward and reverse files during pairing. |
Quick launch
For most local microbiology users, the GUI is the easiest starting point:
```bash conda activate MicroSeq microseq-gui