JBrowse Large Metageone Handler

Usage

Run npm install -force 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

$3

#### 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
``bash
$ gunzip -c ERZ1049444_FASTA.fasta.gz > ERZ1049444_FASTA.fasta
`
##### Step 2: Recompress as BGZF
`bash
$ bgzip ERZ1049444_FASTA.fasta
`
##### To confirm it's BGZF:
`bash
$ file ERZ1049444_FASTA.fasta.gz
`
##### Step 3: Create the FASTA Index
`bash
$ samtools faidx ERZ1049444_FASTA.fasta.gz
`

#### Generating GFF file indexes

##### Step 1: Decompress the BGZF file
`bash
$ bgzip -d -c ERZ1049444_FASTA_annotations.gff.bgz > ERZ1049444_FASTA_annotations.gff
`
##### Step 2: Recompress with Standard Gzip
`bash
$ gzip ERZ1049444_FASTA_annotations.gff
`
##### tabix index
`bash
$ tabix -p gff ERZ1049444_FASTA_annotations.gff.bgz
`
##### Step 3: Generate .ix and .ixx Index Files
`bash
$ jbrowse text-index --file ERZ1049444_FASTA_annotations.gff.bgz --exclude none --attributes interpro,pfam,eggnog
``