MGnify JBrowse NPM Component

Usage

Run npm install and then npm start to start a development instance.

Run npm build which produces a build directory that can be deployed to a static web server

GeneViewer (standalone component)

This repo now exports a GeneViewer React component that provides:

• JBrowse Linear Genome View (assembly + gene track)
• Selected gene highlighting
• Optional essentiality coloring driven by a local CSV (no API/database)
• Feature panel (basic annotations from GFF)
• Synced “genes in view” table (based on current viewport)

Library usage

import { GeneViewer } from 'mgnify-jbrowse'

Demo app configuration (CRA)

The included demo app reads URLs from env vars:

REACT_APP_ASSEMBLY_NAME=your_assembly_name
REACT_APP_FASTA_GZ_URL=https://.../genome.fasta.gz
REACT_APP_FASTA_FAI_URL=https://.../genome.fasta.gz.fai
REACT_APP_FASTA_GZI_URL=https://.../genome.fasta.gz.gzi
REACT_APP_GFF_BGZ_URL=https://.../annotations.gff.bgz
REACT_APP_GFF_TBI_URL=https://.../annotations.gff.bgz.tbi

# Optional:
REACT_APP_ESSENTIALITY_CSV_URL=https://.../essentiality.csv
REACT_APP_GFF_IX_URL=https://.../annotations.gff.bgz.ix
REACT_APP_GFF_IXX_URL=https://.../annotations.gff.bgz.ixx
REACT_APP_GFF_META_URL=https://.../annotations.gff.bgz_meta.json

Generate Indexes

FTP URLs

FASTA File URL: https://www.ebi.ac.uk/metagenomics/api/v1/analyses/MGYA00516474/file/ERZ1049444_FASTA.fasta.gz GFF File URL: https://www.ebi.ac.uk/metagenomics/api/v1/analyses/MGYA00516474/file/ERZ1049444_FASTA_annotations.gff.bgz

Generating FASTA file indexes

Step 1: Decompress the FASTA File

$ gunzip -c ERZ1049444_FASTA.fasta.gz > ERZ1049444_FASTA.fasta

Step 2: Recompress as BGZF

$ bgzip ERZ1049444_FASTA.fasta

To confirm it's BGZF:

$ file ERZ1049444_FASTA.fasta.gz

Step 3: Create the FASTA Index

$ samtools faidx ERZ1049444_FASTA.fasta.gz

Generating GFF file indexes

Step 1: Decompress the BGZF file

$ bgzip -d -c ERZ1049444_FASTA_annotations.gff.bgz > ERZ1049444_FASTA_annotations.gff

Step 2: Recompress with Standard Gzip

$ gzip ERZ1049444_FASTA_annotations.gff

tabix index

$ tabix -p gff ERZ1049444_FASTA_annotations.gff.bgz

Step 3: Generate .ix and .ixx Index Files

$ jbrowse text-index --file ERZ1049444_FASTA_annotations.gff.bgz --exclude none --attributes interpro,pfam,eggnog