Support

Help opening genomes, alignments, and annotations in JGV on iPhone and iPad.

Open a genome

1. Put files in the Files app, or keep them in iCloud Drive.
2. In JGV, open Tracks and choose Open genome.
3. Select the FASTA (.fa, .fasta, .fna). If there is no .fai, JGV builds one.

On iOS, Files often hides the last extension. A 176-byte TAIR10.fa.fai can look like TAIR10.fa. Pick the large sequence file, not the tiny index.

Add tracks

• Alignments — SAM opens as-is. BAM builds a .bai if missing. CRAM needs an existing .crai beside it, and an uncompressed FASTA already open.
• Features — GFF3 / GTF and BED.
• Variants — VCF.
• Signal — BigWig.
• Contacts — BEDPE (cis heatmap).

When you can, select a data file and its index together. If the system picker only copies an index, JGV will look next to it in the app Documents folder for the matching FASTA or BAM.

Indexes

• FASTA without .fai — JGV writes a samtools-style index.
• BAM without .bai — JGV builds one. Large BAM files can take a while the first time.
• CRAM without .crai — not built in-app. Create it on a computer with samtools index sample.cram and copy both files in.

Clear loaded data

Tracks → Clear loaded data, Settings → Clear loaded data, or the ⋯ menu. This unloads the genome and tracks. Files on disk stay. Use it before opening a different species so leftover chromosomes do not confuse the viewer.

Ads and tracking

JGV is free and may show an app-open ad after you return from the background. The first launches stay ad-free. iOS will ask whether JGV may track across apps for more relevant ads. Either answer is fine; the browser still works. See the Privacy Policy.

JGV is not IGV

JGV is an independent Japality product. It is not affiliated with the Integrative Genomics Viewer (IGV) or the Broad Institute.