mothur

TAFFISH tool app for mothur, the microbial community analysis package for amplicon sequence processing, OTU/ASV-oriented workflows, taxonomy assignment, and ecological summaries.

Package Identity

• App name: mothur
• Command: taf-mothur
• TAFFISH version: 1.48.5-r1
• App kind: tool
• Container image: ghcr.io/taffish/mothur:1.48.5-r1
• Runtime source: official GitHub release noReadline binaries
• Upstream version: 1.48.5
• Upstream release tag: v1.48.5
• Upstream license: GPL-3.0-only
• TAFFISH wrapper license: Apache-2.0

What This App Packages

This app packages the official mothur v1.48.5 Linux noReadline release assets for native linux/amd64 and linux/arm64.

Common runtime contents:

• mothur: the upstream mothur command
• taf-mothur-entrypoint: a thin TAFFISH-safe adapter for --run and --batch
• vsearch: helper bundled in the image for mothur commands and smoke checks
• uchime: helper bundled in the image for mothur commands and smoke checks

The upstream linux_x86_64 noReadline asset also includes prefetch and fasterq-dump. They are preserved when present in that official asset, but they are not part of the portable cross-platform app contract because the upstream linux_arm64 noReadline asset does not ship them. Treat SRA download workflows as explicit, networked data-preparation steps rather than as default TAFFISH runtime behavior.

The release assets are downloaded from GitHub and verified during image build:

linux/amd64 Mothur.linux_x86_64.noReadline.zip
4f96690066a6bc8405abb0fd9503ae07dc6581711cdf83d21c8aa3245be5ec0d

linux/arm64 Mothur.linux_arm64.noReadline.zip
a25109dec86ce5dacea62594531c6a31f630ae88a05ef5632a860bb515d78abf

Runtime source metadata is preserved at:

/opt/mothur/share/doc/mothur/source.txt

Scope

Supported through upstream mothur commands and batch files:

• sequence summaries and quality inspection, such as summary.seqs
• read merging and amplicon preprocessing, such as make.contigs
• dereplication and count/name table generation, such as unique.seqs
• chimera checking through mothur commands that use bundled helpers
• taxonomy assignment with user-provided reference FASTA and taxonomy files
• distance, clustering, OTU/ASV-oriented tables, and ecological summaries
• mothur batch files for complex or multi-step command syntax

This app does not:

• bundle production taxonomy databases such as SILVA, RDP, UNITE, or custom project references
• provide a new TAFFISH microbiome pipeline or choose mothur workflow defaults
• guarantee cross-platform SRA Toolkit helper availability
• perform runtime network downloads in smoke tests or ordinary examples
• replace the upstream mothur manual or scientific validation of a workflow

Usage

Check runtime identity:

taf-mothur --run get.current

Show upstream help:

taf-mothur --run help
taf-mothur --run summary.seqs help

Run simple mothur commands through the safe adapter:

taf-mothur --run summary.seqs fasta=reads.fasta
taf-mothur --run unique.seqs fasta=reads.fasta
taf-mothur --run make.contigs file=stability.files processors=8

Run a mothur batch file:

taf-mothur --batch commands.batch
taf-mothur commands.batch

Example commands.batch:

summary.seqs(fasta=reads.fasta)
unique.seqs(fasta=reads.fasta)
chimera.vsearch(fasta=reads.unique.fasta, count=reads.count_table)

Use batch files for complex mothur syntax, multiple commands, comments, spaces, or parameter values that contain shell metacharacters.

Command Mode And Quoting

Most TAFFISH tool apps use <taf-app:container:...> with automatic command mode. This app intentionally does not.

mothur's own CLI commonly accepts raw command strings such as #summary.seqs(fasta=reads.fasta). Those strings contain # and parentheses, which cannot be safely represented by plain ::*ARGV*:: in generated shell. The wrapper therefore calls a thin adapter:

<container:ghcr.io/taffish/mothur:1.48.5-r1>
taf-mothur-entrypoint ::*ARGV*::

Use --run COMMAND key=value ... for simple commands; the adapter constructs the mothur command string inside the container. Use --batch FILE for the full upstream batch-file interface.

This also means taf-mothur vsearch ... and taf-mothur uchime ... are not the supported direct-call interfaces. The bundled helper executables are present for mothur commands and image-level validation. Use the separate taf-vsearch app when you need to run VSEARCH directly.

Inputs And Outputs

Common inputs:

• FASTA and FASTQ files, including amplicon reads and assembled contigs
• mothur count, name, group, list, taxonomy, and design tables
• oligos/files manifests used by mothur workflows
• taxonomy reference FASTA and taxonomy files supplied by the user
• mothur batch files or --run command arguments

Common outputs:

• .summary files from sequence summary commands
• .unique.fasta and count tables from dereplication steps
• taxonomy and classification outputs
• distance, list, shared, rarefaction, and ecological summary outputs
• mothur.*.logfile files produced by upstream mothur

Output names and locations follow upstream mothur behavior. For reproducible projects, set mothur input/output directories explicitly in your batch file or run the wrapper from the intended output directory.

Databases, References, And Network

mothur workflows often require taxonomy references and training sets, for example SILVA, RDP, UNITE, or project-specific reference files. This app does not bundle those production references because they are large, updated independently, and workflow-specific.

Mount or place reference files in the working directory and pass their paths to mothur commands, for example:

taf-mothur --run classify.seqs fasta=reads.fasta count=reads.count_table reference=silva.fasta taxonomy=silva.tax

No network access is required at runtime for ordinary local mothur workflows after inputs and references are available. SRA download-oriented workflows should be treated as explicit data acquisition outside the smoke-tested core.

Platform And Resources

The app builds native images for linux/amd64 and linux/arm64 from official mothur release assets. Resource usage depends on read count, reference size, distance calculation, clustering strategy, and thread settings in mothur commands.

Use mothur's own processors parameters where applicable to keep CPU use predictable in shared environments.

Testing

The smoke coverage checks:

• wrapper metadata and TAFFISH help
• adapter behavior for --run and --batch
• upstream version banner for mothur v.1.48.5
• upstream help for summary.seqs
• bundled vsearch and uchime availability
• dynamic library closure for the packaged executable set
• a tiny offline FASTA workflow covering summary.seqs and unique.seqs

The smoke test is intentionally independent and uses only data generated inside a temporary directory. It does not replace full scientific validation of a microbiome analysis protocol, database choice, primer/oligos policy, taxonomy reference version, or ecological interpretation.

License And Citation

The TAFFISH packaging code and documentation are distributed under Apache-2.0.

Upstream mothur is distributed under GPL-3.0-only according to the upstream license file. Its license is preserved under:

/opt/mothur/share/licenses/mothur/LICENSE

Please cite:

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology. 2009;75:7537-7541. DOI: 10.1128/AEM.01541-09.

Additional citations may be appropriate for specific mothur algorithms and workflow choices; follow upstream documentation for method-specific citation guidance.

Upstream Resources

• mothur homepage: https://mothur.org/
• mothur manual: https://mothur.org/wiki/mothur_manual/
• GitHub repository: https://github.com/mothur/mothur
• v1.48.5 release: https://github.com/mothur/mothur/releases/tag/v1.48.5