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Sanger Sequence QC & Alignment

Sanger Sequence QC: review Sanger sequence quality before downstream work.

Turn Sanger files into trimmed sequences, quality evidence and an exact mismatch table.

START HEREChoose documentsAB1, ABI, FASTA, FA, FASTQ, FQ
Choose documents Try prepared example
Maximum
64 files · 64 MB total
File handling
Draft 2 hours · encrypted result 24 hours
FREE3 jobs a dayFiles up to 10 MB
PROUp to 200 jobs a day€12.99/month or €89.99/year
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Larger files need Pro. Failed jobs are never counted.

  • Prepared example is free
  • 3 free jobs a day
  • Cancel anytime
EXAMPLE RESULTSample data
Reads · 24
21
14,382
24
Trimmed bases · 14,382
Three reads fail the confirmed quality profileHTML, trace plots, trimmed FASTA, QC CSV, pairwise alignment evidence, JSON and manifest
Reads
24
Passed
21
Trimmed bases
14,382
Formats, limits & file handling
Works with
AB1, ABI, FASTA, FA, FASTQ, FQ
Limit
64 files · 64 MB total
You receive
HTML, trace plots, trimmed FASTA, QC CSV, pairwise alignment evidence, JSON and manifest
File handling
Draft 2 hours · encrypted result 24 hours

Turn Sanger files into trimmed sequences, quality evidence and an exact mismatch table.

THREE CLEAR STEPS

From your documents to a usable result.

  1. 01
    Add your input

    Limits and supported formats are visible before you begin.

  2. 02
    Review the result

    Check the preview, findings or artwork before you download.

  3. 03
    Download

    Use your free job, plan or credits. Failed jobs are never counted.

Prepared result preview

See the decision before sharing a real file.

Turn Sanger files into trimmed sequences, quality evidence and an exact mismatch table. This prepared example uses fictional data and the same evidence structure as the server export.

✓
Nothing is uploadedPublic demo only

Sequence QC

Three reads fail the confirmed quality profile

Parameters and coverage remain visible; output is research-use-only and never a diagnostic interpretation.

Actual prepared coverage: AB1 and FASTQ · QC only unless a reference source number is confirmed

  • ErrorTrimmed read too shortsample-07.ab1 · 41 bases below confirmed 50
  • WarningAmbiguous bases above limitsample-19.ab1 · 8.4% N versus 5%
  • EvidenceConfirmed-reference alignmentWhen enabled, the selected source number and pairwise results are recorded
Reads
24
Passed
21
Trimmed bases
14,382
Show the verified package

HTML, trace plots, trimmed FASTA, QC CSV, pairwise alignment evidence, JSON and manifest

Engine sanger-sequence-qc-v1 · rules sanger-qc-parameters-2026-08-30

One focused workflow

From bounded input to evidence you can review

  1. Add the source.Accepted inputs are AB1, ABI, FASTA, FA, FASTQ, FQ. The visible limit is 64 files · 64 MB total.
  2. Confirm the job.Every assigned source number, selected filename and setting stays visible before the confirmed SHA-256 input hash is accepted. Product-specific mappings remain explicit settings rather than guessed roles.
  3. Process in isolation.A one-job networkless sandbox receives only this job and cannot access accounts, queues, encryption keys or other customer storage.
  4. Review exact findings.Check trace or sequence quality, trim by fixed parameters and align against an optional reference with mismatch evidence.
  5. Download the evidence.HTML, trace plots, trimmed FASTA, QC CSV, pairwise alignment evidence, JSON and manifest Every output hash is covered by the coordinator-created manifest.

What this product does not claim

Parameters and coverage remain visible; output is research-use-only and never a diagnostic interpretation.

Clear answers

Sanger Sequence QC & Alignment FAQ

Which sequence files are accepted?

AB1 and ABI trace files plus FASTA and FASTQ sequences, up to 64 files and 64 MB per job.

How is trimming decided?

By the fixed quality parameters you confirm before the run, applied identically to every read. The report shows how many bases each read kept after trimming.

What makes a read fail the quality profile?

A trimmed length below the confirmed minimum, or ambiguous base calls above the allowed share. Each failure is listed with the file name and the measured value.

Is a reference sequence required?

No. Quality control runs on its own. Alignment and the pairwise mismatch table appear only when you confirm a reference to align against.

Can the result support a diagnosis?

No. The output is research use only. It documents quality, trimming and mismatches without interpreting what they mean for a patient or a sample.

Available now

Review Sanger sequence quality before downstream work.

Inspect the fictional result now. Your own files run here without an account: 3 free jobs a day, or up to 200 a day with Pro.

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