What's my (human) genome?

Powered by ref-solver - Identify HUMAN reference genomes from sequence headers and files

📖 Help & Documentation ▼

How ref-solver Works

ref-solver identifies reference genomes by analyzing sequence headers and comparing them against a curated catalog of known references. It uses multiple matching strategies:

  • MD5 checksums - Most accurate method for exact sequence matching
  • Name + length - Matches contigs by identifier and sequence length
  • Alias matching - Handles different naming conventions (chr1 vs 1, etc.)
  • Order analysis - Detects if contigs are reordered

The tool provides confidence scores and actionable suggestions for handling mismatches.

Supported Input Types

SAM Header: Paste @SQ lines directly or upload .sam files

Sequence Dictionary: Upload Picard .dict files from reference preparation

Assembly Report: Upload NCBI assembly reports with comprehensive metadata

VCF Header: Upload VCF files to extract ##contig lines

FASTA Index: Paste or upload .fai index files (5 tab-separated columns)

BAM/CRAM/FASTA: Upload binary files (.bam, .cram, .fa, .fasta) to extract headers automatically

All formats are automatically detected and parsed appropriately.

Understanding Results

Confidence Levels:

  • Exact - Perfect match, safe to use
  • High - Very good match with minor differences
  • Medium - Good match but needs attention
  • Low - Poor match, likely wrong reference

Match Types: Exact, Renamed, Reordered, Partial, Mixed, No Match

Suggestions: Actionable commands for fixing common issues like renaming or reordering contigs

Input & Configuration

▼
Paste SAM header lines (@SQ), FASTA index, or upload .sam, .dict, or .fai files.
Paste NCBI assembly report content or upload assembly report files (.txt/.tsv) with comprehensive sequence metadata.
Paste VCF contig header lines (##contig) or upload VCF files to extract reference information.
Upload BAM, CRAM, or FASTA files to automatically extract sequence information from headers. These files are uploaded and processed server-side.

Configuration

80%

Scoring Weights

40%
30%
20%
10%

Note: Weights are automatically normalized to sum to 100% during scoring.

ref-solver by Fulcrum Genomics