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Taxonomy~10 min

What is the taxonomic composition of my samples?

Species profileDiversityAbundance table

2 compatible inputsConfigure

Get interpretable results

Species profile

relative abundance

Bacteroides spp.

38%

Firmicutes

24%

Lachnospiraceae

18%

Result based Manuscript

Microbiome · Vol 14 · Art 028Open access

Gut microbial dominance and AMR carriage in healthy human stool metagenomes

S. Valenzuela, J. Pérez, A. Lin · QuestOmics Research

Abstract

We profiled 12.4M paired-end reads from Stool_028 using a shotgun-mgx pipeline. Bacteroides vulgatus dominates the community (38%), with Shannon 3.84 indicating high evenness. Two AMR markers (blaTEM-1, tetM) were detected at low coverage.

Methods · v1.4 · 95% conf.View PDF

Turn gut microbiome data into publication-ready materials

Choose the biological questions you care about instead of assembling bioinformatics pipelines. QuestOmics turns your sequencing data into interpretable results, publication-ready figures, and methods for human gut microbiome studies.

Your metadata, read the way you keep it.

Upload the spreadsheet as it is. We match every row to the right sequencing file, then turn on the comparisons your columns can actually support.

Upload your metadataWe parse itYour comparisons switch on

metadata.tsv

142 of 142 matched

Stool-21S21_R1.fastq.gzMatched
Stool_23bS23b_R1.fastq.gzLikely 91%

Nobody writes sample names the same way twice. We match across separators, capitals, read-pair suffixes, and typos, and hand back anything we cannot place with confidence.

Smart header mapping

CSV, TSV, Excel

sample_id

Sample

group

Condition

antibiotics

Kept

age

Kept

site

Kept

We find the column that holds your sample names by reading the values inside it, so its header can say anything you like, and we take the first guess at your condition column. Trailing spaces, blank columns and duplicate headers are cleaned on upload, and column names are normalized to the character set R and Python accept before the run starts, so the tools downstream do not choke on them.

Guardrails for the stats downstream

2 ready

group/responder 12, non responder 11Ready to compare
antibiotics/yes 9, no 14Ready to compare
site/clinic 21, home 2Needs 3 per group

Before you spend a single ATP, we count the samples behind every group. Differential abundance, the volcano plot included, needs at least three samples per group across at least two groups. A column that falls short keeps its card locked and names the group that is too small, so you find out while you are setting the run up.

Every interpretation cites the papers it actually used.

Gut Assistant reads published gut microbiome research and can only speak from what it retrieves and from your own results.

The library it reads

Indexed

AbstractResultsDiscussionConclusion

Left out

ReviewsMeta-analysesCase reports

Open-access primary research on the gut microbiome. When the library grows, you can re-run against the newer papers.

How it finds the papers

Three signals, one ranking.highmediumlowconfidence, on every answer

Every claim shows its source

Prevotella copri was elevated in the responder group (q = 0.003) your data and is reported to comprise four clades that differ in gene content [E1].

[E1]Tett A, et al. (2019). Cell Host Microbe. doi:10.1016/j.chom.2019.08.018

Teal marks a number from your analysis.
Violet opens the passage it read.
Papers it did not cite never reach the list.

Where to send it

Bonus

1Microbiome91

2Gut Microbes84

3mSystems76

Cover letterReviewersKeywords

We score your manuscript against the recent papers of each venue, then draft the cover letter and suggest reviewers for the one you pick.

You never have to open the machine room.

Each analysis runs inside a sealed container image, and the run keeps a record of the tools, the versions and the settings that produced it. That record is what your Methods section is written from.

WORKS WITHIlluminaOxford NanoporePacBio

What you never see

One analysis

Inside the containerapptainer run --cleanenv

Dashed boxes are reference databases we host for you.

What you see

All of it, behind one button

Run analysis Taxonomic profiling12 samples

Not your job

install the toolsmanage condabook a cluster nodemind the scratch disk

A pipeline like this one sits behind every analysis you can pick, and it runs on our compute. Nothing to install, no queue to watch, no reference database to download. You choose the analysis and the samples, and that is the whole job.

It comes back out as your Methods

Versioned

Taxonomic profiles were generated with MetaPhlAn (v4.2.2; Blanco-Míguez et al., 2023) after quality filtering with fastp (v1.3.0; Chen et al., 2018) and host read removal against GRCh38 with minimap2 (v2.28; Li, 2018). Differential abundance was tested with MaAsLin3 on the group column, using non responder as the reference group.

References

1.Blanco-Míguez A, et al. (2023). Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature Biotechnology 41:1633. doi:10.1038/s41587-023-01688-w
2.Chen S, Zhou Y, Chen Y, Gu J (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884. doi:10.1093/bioinformatics/bty560
3.Li H (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094. doi:10.1093/bioinformatics/bty191

Copy paragraphDOCXPDFFigures

Nothing here is typed by hand. The versions and the citations come from the record of the run. If a version was never recorded, the text says [not recorded] instead of inventing one.

And it comes back out as your Results

Enriched in responders
Depleted
Not significant

Figure 1. Volcano plot of the species that differ between responders and non-responders. Dashed lines mark the cutoffs the run used, q = 0.05 and a two-fold change.

Nothing here is drawn by hand either. Every point comes from the run that wrote the paragraph above, and the table the figure was drawn from is there to download.

No analysis is locked behind a plan.

Every plan can run every analysis on the platform. You spend ATP to launch one, and each plan gives you an amount of it every month. What you pay for is how much you can run, how large your files can be, and how much help you get.

Monthly billing is also available, at €15 and €99 per month.

More than five people, or a core facility? Talk to us.

Included on every plan

Every analysis in the catalogue runs on every plan. There is no tier that unlocks one.
Delete a sample and its space comes back on the spot.
Unspent ATP carries forward month to month. On Lab the balance is held at 200 ATP.
You can buy ATP packs at any time, on any plan, including Free.

What ATP buys

Run an analysis: Cost shown before you launch
First interpretation of a run: 0 ATP
Ask for that interpretation again: 1 ATP
Manuscript draft: 0, 1 or 2 ATP

You pick the manuscript draft depth on each run.

Free

€0

Always free

The base

ATP each month7

Plus 10 more, once, when you sign up.

Journal fit, cover letter and reviewer suggestions: 1 ATP each
Figure export with no watermark: 1 ATP per run

Up to 3 GB per file

No card needed.

Researcher

Start with one question.

Upload a sequencing run, choose the analysis you want, and read the answer with its sources beside it. The free plan comes with 7 ATP a month and 10 more when you sign up, and it does not ask for a credit card.