Savage Bioinformatics

Genomic analysis · Client report

Bacterial Whole-Genome Sequencing Analysis Report

Sample Vibrio-AlPipeline v1.0.0

Pipeline status
COMPLETED

Computational workflow execution

Data quality
REVIEW RECOMMENDED

Independent QC and assembly screening

Sample ID
Vibrio-Al
Analysis date
14 September 2026, 13:41 UTC
Report type
Automated bacterial WGS
01 · At a glance

Executive summary

Core read, assembly, and annotation metrics from this run. Quality flags are summarized separately below.

Input read pairs
252,200
Validated paired reads
Retained paired reads
170,848
After trimming
Read survival
67.7%
67.743% exact
Assembly size
4.80 Mb
4,803,858 bp total
Contig count
2,236
QUAST contigs
N50
2,964 bp
Assembly continuity
GC content
44.57%
Whole assembly
CDS count
4,162
Bakta predictions
02 · Process

Analysis workflow

Stage completion and quality warnings are shown together here, while remaining distinct in the report header.

  1. Raw QCFastQCReview
  2. TrimmingTrimmomaticCompleted
  3. Post-trim QCFastQCReview
  4. AssemblySPAdesReview
  5. Assembly QCQUASTReview
  6. AnnotationBaktaCompleted
  7. ReportingSummaryCompleted
03 · Review

Quality assessment

Automated screening supports expert review; it does not determine organism identity, clinical significance, or suitability for every downstream use.

Sequencing quality

REVIEW RECOMMENDED
Raw FastQCFAIL
Post-trim FastQCFAIL
Reads retainedpaired reads170,848
Paired-read survival67.743%

Assembly quality

Review
Genome assembly size4,803,858 bp
Contigs2,236
Largest contig44,753 bp
N50 / L502,964 bp / 484
GC content44.57%
04 · Evidence

Visual summary

Compact, report-native visualizations generated only from available pipeline metrics.

Reads before and after trimming

Read pairs
Input read pairs252,200
Retained paired reads170,848

67.7% of input pairs retained. Bar lengths use input pairs as the reference.

Assembly metric profile

QUAST
Contig count2,236reported by QUAST
Largest contig44,753 bp
N502,964 bp

Bar lengths compare N50 with the largest contig; they are descriptive, not acceptance thresholds. N50 is 0.06% of assembly length.

Contig length distribution

Log scale
219 contigs245 contigs260 contigs274 contigs253 contigs267 contigs201 contigs206 contigs125 contigs94 contigs49 contigs23 contigs13 contigs5 contigs1 contigs0 contigs0 contigs1 contigs500 bpmedian 1,518 bp44,753 bp

Distribution of 2,236 assembly FASTA records ≥500 bp. The horizontal axis is logarithmic.

Per-contig GC distribution

Assembly FASTA
2 contigs1 contigs6 contigs6 contigs11 contigs26 contigs47 contigs102 contigs208 contigs362 contigs465 contigs422 contigs317 contigs158 contigs75 contigs19 contigs6 contigs3 contigs30.2%median 44.7%54.5%

Unweighted per-contig GC percentages for the same 2,236 records; this is distinct from whole-assembly GC.

FastQC status summary

Module screening
Raw FastQC R1FAIL

6 pass · 3 warning · 2 fail modules

Raw FastQC R2FAIL

6 pass · 3 warning · 2 fail modules

Post-trim FastQC R1FAIL

8 pass · 1 warning · 2 fail modules

Post-trim FastQC R2FAIL

8 pass · 1 warning · 2 fail modules

Raw reads22 checks across 2 reads
12 pass6 warning4 fail
Post-trim reads22 checks across 2 reads
16 pass2 warning4 fail
05 · Features

Annotation summary

Gene-feature predictions from Bakta. Predicted features should be reviewed in the context of the assembly quality.

COMPLETEDCoding sequences4,162Bakta CDS predictions

Annotation deliverables

Bakta annotation completed using the configured database.

Annotation statusCOMPLETED
Total features4,262
↓GFF3↓GBFF↓FAA↓FFN↓TSV↓JSON
06 · Deliverables

Download center

Organized analysis outputs. Links are relative and remain portable with the complete sample results directory.

Quality control

Read-level and combined QC outputs

HTMLMultiQC overviewCombined interactive quality-control reportHTMLRaw FastQC R1Per-read FastQC reportHTMLRaw FastQC R2Per-read FastQC reportHTMLTrimmed FastQC R1Per-read FastQC reportHTMLTrimmed FastQC R2Per-read FastQC report

Assembly

Assembled sequence and continuity assessment

FASTAAssembly FASTASPAdes assembled contig sequencesHTMLQUAST reportInteractive assembly quality report

Annotation

Bakta feature annotations and sequences

GFF3GFF3Genome features and coordinatesGBFFGenBank flat fileAnnotated genome sequenceFAAProtein FASTAPredicted amino-acid sequencesFFNFeature nucleotide FASTANucleotide sequences of annotated featuresTSVAnnotation TSVTabular Bakta annotationsJSONAnnotation JSONStructured Bakta annotations

Machine-readable results

Portable outputs for analysis and archiving

JSONSummary JSONComplete structured result summaryTSVSummary TSVCompact tabular result summary

Technical information / reproducibility

Tool versions, inputs, parameters, and execution timestamps

Software environment

FastQC0.12.1
MultiQC1.35
Trimmomatic0.41
SPAdes4.3.0
QUAST5.3.0
Baktabakta 1.11.4
PyHMMER0.11.4
Nextflow26.04.6
WGS pipeline1.0.0
Bakta databaseNot recorded in summary

Run provenance

Pipeline started14 September 2026, 13:41 UTC
Summary completed14 September 2026, 13:41 UTC
Forward inputVibrio-Al_L001_R1_001.fastq
Reverse inputVibrio-Al_L001_R2_001.fastq
Pipeline version1.0.0

Trimming parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50

Quality-screening heuristic: Review is recommended when FastQC reports warning/failure flags, or when an assembly has ≥500 contigs and N50 is <1% of total assembly length. This heuristic is an advisory flag, not a biological acceptance threshold.