Import a BAM or SAM File

How do I import a BAM or SAM assembly into SnapGene?

Import or Open an Appropriate Reference Sequence

SAM and BAM formats are map to reference assembly formats. A fasta format reference sequence is often output with a SAM or BAM file.

Note that SnapGene treats a SAM or BAM file as a list of reads for realignment to the reference. SnapGene ignores alignment coordinates present in the alignment file and realigns all reads to the reference file using the SnapGenes "align to reference" algorithm.

NOTE: SnapGene is not designed to import or handle NGS assemblies.

Import your reference sequence fasta, or open an appropriate reference sequence file.

Import the Assembly alignment File

Click SnapGene menu Tools → Align to Reference DNA Sequence → Align Imported Sequences....

Use the File Browser to select the appropriate SAM or BAM alignment file then click Open.

Confirm the Alignment has Imported Correctly.

The reads defined by the assembly file will import onto the reference. SnapGene will trim all reads (if quality information is present) and realign all reads to the reference sequence.