illumina_coordinates
| Crates.io | illumina_coordinates |
| lib.rs | illumina_coordinates |
| version | 0.9.1 |
| source | src |
| created_at | 2018-04-26 04:00:27.647722 |
| updated_at | 2018-08-19 15:04:49.753153 |
| description | Parses Illumina sequence identifiers found in FASTQ files |
| homepage | |
| repository | https://github.com/jimrybarski/illumina-coordinates |
| max_upload_size | |
| id | 62334 |
| size | 13,318 |
Jim Rybarski (jimrybarski)
documentation
README
illumina_coordinates
In FASTQ files created by the Illumina sequencing process, the sequence identifiers contain the coordinates of the DNA cluster that produced the sequence (among other things). This library parses the identifiers.
Usage
extern crate illumina_coordinates;
fn main() {
let line = "@M03745:11:000000000-B54L5:1:2108:4127:8949";
let seq_id = illumina_coordinates::parse_sequence_identifier(&line).unwrap();
assert_eq!(seq_id.sequencer_id, "M03745".to_string());
assert_eq!(seq_id.run_count, 11);
assert_eq!(seq_id.flow_cell_id, "000000000-B54L5".to_string());
assert_eq!(seq_id.lane, 1);
assert_eq!(seq_id.side, 2);
assert_eq!(seq_id.swath, 1);
assert_eq!(seq_id.tile, 8);
assert_eq!(seq_id.x, 4127);
assert_eq!(seq_id.y, 8949);
}
Description of Fields
Take this example sequence identifier:
@M03745:11:000000000-B54L5:1:2108:4127:8949
| Value | Meaning |
|---|---|
M03745 |
ID of the sequencing machine |
11 |
run count for this machine |
000000000-B54L5 |
ID of the flow cell. "B54L5" will be printed on the flow cell in this example |
1 |
lane number. For MiSeqs, there's only one lane |
2 from 2108 |
the side of the chip |
1 from 2108 |
the swath (for MiSeqs, this is always 1. For HiSeqs, each lane is two tiles wide, and the first pass from left-to-right is swath one, then the returning pass on the other side of the lane is swath two |
08 from 2108 |
the tile number. For MiSeqs, this is a number from 1 to 19 |
4127 |
the x-position of the read in the tile, in arbitrary units |
8949 |
the y-position of the read in the tile, in arbitrary units |
See https://help.basespace.illumina.com/articles/descriptive/fastq-files/ for more information.