Skip to content

Commit

Permalink
Merge pull request #4 from will-rowe/master
Browse files Browse the repository at this point in the history 
Add insert.bed for each scheme
  • Loading branch information
Will Rowe authored Aug 27, 2020
2 parents 7d51020 + 6f82eb0 commit 160a1db
Show file tree
Hide file tree
Showing 9 changed files with 922 additions and 28 deletions.
416 changes: 395 additions & 21 deletions LICENSE
View file

Large diffs are not rendered by default.

60 changes: 60 additions & 0 deletions Nipah/V1/NiV_6_Malaysia.insert.bed
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,60 @@
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 27 378 1 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 341 702 2 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 662 1004 3 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 965 1308 4 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 1263 1617 5 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 1567 1900 6 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 1862 2212 7 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 2204 2538 8 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 2501 2831 9 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 2820 3156 10 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 3138 3471 11 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 3457 3795 12 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 3740 4089 13 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4037 4364 14 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4305 4652 15 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4596 4924 16 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4907 5246 17 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 5197 5567 18 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 5522 5873 19 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 5814 6145 20 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 6103 6462 21 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 6429 6760 22 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 6733 7072 23 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 7048 7385 24 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 7368 7708 25 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 7682 8027 26 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 7956 8284 27 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 8267 8604 28 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 8526 8869 29 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 8850 9191 30 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 9178 9506 31 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 9482 9829 32 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 9773 10124 33 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 10100 10441 34 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 10408 10735 35 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 10698 11029 36 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 10965 11308 37 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 11283 11614 38 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 11550 11881 39 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 11813 12151 40 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 12123 12469 41 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 12403 12749 42 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 12737 13074 43 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 13053 13384 44 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 13368 13704 45 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 13694 14028 46 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 13990 14325 47 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 14304 14651 48 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 14617 14946 49 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 14888 15228 50 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 15171 15534 51 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 15506 15855 52 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 15806 16173 53 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 16126 16455 54 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 16433 16758 55 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 16733 17077 56 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 17061 17399 57 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 17362 17701 58 2 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 17691 18025 59 1 +
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 17836 18166 60 2 +
48 changes: 41 additions & 7 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,37 @@

Primer schemes for real-time genome epidemiology

[![Build Status](https://travis-ci.org/will-rowe/primer-schemes.svg?branch=master)](https://travis-ci.org/will-rowe/primer-schemes)
[![Build Status](https://travis-ci.org/artic-network/primer-schemes.svg?branch=master)](https://travis-ci.org/artic-network/primer-schemes)
[![DOI](https://zenodo.org/badge/x.svg)](https://zenodo.org/badge/latestdoi/x)

## updated scheme file format
## About

The primer schemes in this repository were built using [Primal Scheme](https://primalscheme.com/) and are available for the following viruses:

- Ebola
- Nipah
- SARS-CoV-2

Within each virus directory, there are versioned sub-directories which each contain a versioned scheme for that virus.

The following files are available per scheme version:

| file extension | about |
| ------------------ | -------------------------------------------------------------------------------------- |
| `.primer.bed` | The coordinates of each primer in the scheme |
| `.insert.bed` | The coordinates of the expected amplicons that the scheme produces (excluding primers) |
| `.reference.fasta` | The sequence of the reference genome used for the scheme |
| `.tsv` | Details on each primer in the scheme (name, sequence, length, GC, TM) |

For more information visit the [ARTIC network website](https://artic.network/).

## Notes

- There may be some additional files in the scheme directories - these are either deprecated and left for backward compatibility (e.g. `scheme.bed`), or are created by Primal Scheme [check here](https://github.com/aresti/primalscheme) for more info.
- The schemes are in BED format, which is a 0-based, half-open format. This means that reference sequence position counting starts at 0 and the chromEnd is not included in the primer sequence.
- All the schemes within this repository can be downloaded using [artic-tools](https://github.com/will-rowe/artic-tools) (e.g. `artic-tools get_scheme ebola --schemeVersion 2`)

## Updated scheme file format

> updated: 25.08.2020
Expand All @@ -28,12 +55,19 @@ The new format has the following columns:

<sup>\*</sup> column 5 in the BED spec is an int for score, whereas here we are using it to denote primerPool.

### liftover
### commands

The `liftover.py` script was used to create files in the new format for existing schemes in this repository.
The `liftover.py` script was used to create a `*.primer.bed` file for each `*.scheme.bed` file, within each scheme directory in this repository.

Schemes were updated using the following command:
The `validate_scheme` command from [artic-tools](https://github.com/will-rowe/artic-tools) was used to validate each `*.primer.bed` and also to create the `*.insert.bed` file which is produced by recent versions of [Primal Scheme](https://github.com/aresti/primalscheme).

```
for i in */V*/*.scheme.bed; do scripts/liftover.py -i $i -o ${i%%.scheme.bed}.primer.bed; done;
The following commands where used:

```bash
for i in */V*/*.scheme.bed;
do
basename=${i%%.scheme.bed}
scripts/liftover.py -i $i -o ${basename}.primer.bed;
artic-tools validate_scheme ${basename}.primer.bed --outputInserts ${basename}.insert.bed
done;
```
98 changes: 98 additions & 0 deletions SARS-CoV-2/V1/nCoV-2019.insert.bed
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,98 @@
MN908947.3 54 385 1 1 +
MN908947.3 342 704 2 2 +
MN908947.3 664 1004 3 1 +
MN908947.3 965 1312 4 2 +
MN908947.3 1264 1623 5 1 +
MN908947.3 1595 1942 6 2 +
MN908947.3 1897 2247 7 1 +
MN908947.3 2205 2568 8 2 +
MN908947.3 2529 2882 9 1 +
MN908947.3 2850 3183 10 2 +
MN908947.3 3166 3507 11 1 +
MN908947.3 3482 3826 12 2 +
MN908947.3 3795 4142 13 1 +
MN908947.3 4077 4428 14 2 +
MN908947.3 4321 4674 15 1 +
MN908947.3 4658 4995 16 2 +
MN908947.3 4966 5296 17 1 +
MN908947.3 5259 5620 18 2 +
MN908947.3 5586 5932 19 1 +
MN908947.3 5894 6247 20 2 +
MN908947.3 6196 6528 21 1 +
MN908947.3 6495 6846 22 2 +
MN908947.3 6745 7092 23 1 +
MN908947.3 7058 7389 24 2 +
MN908947.3 7332 7671 25 1 +
MN908947.3 7651 7997 26 2 +
MN908947.3 7968 8319 27 1 +
MN908947.3 8275 8635 28 2 +
MN908947.3 8619 8954 29 1 +
MN908947.3 8913 9245 30 2 +
MN908947.3 9226 9557 31 1 +
MN908947.3 9502 9834 32 2 +
MN908947.3 9806 10146 33 1 +
MN908947.3 10099 10437 34 2 +
MN908947.3 10384 10737 35 1 +
MN908947.3 10688 11048 36 2 +
MN908947.3 11022 11372 37 1 +
MN908947.3 11331 11668 38 2 +
MN908947.3 11584 11927 39 1 +
MN908947.3 11889 12234 40 2 +
MN908947.3 12133 12465 41 1 +
MN908947.3 12439 12779 42 2 +
MN908947.3 12732 13074 43 1 +
MN908947.3 13027 13378 44 2 +
MN908947.3 13344 13669 45 1 +
MN908947.3 13621 13962 46 2 +
MN908947.3 13946 14271 47 1 +
MN908947.3 14232 14579 48 2 +
MN908947.3 14570 14898 49 1 +
MN908947.3 14895 15224 50 2 +
MN908947.3 15193 15538 51 1 +
MN908947.3 15503 15861 52 2 +
MN908947.3 15851 16186 53 1 +
MN908947.3 16144 16485 54 2 +
MN908947.3 16444 16804 55 1 +
MN908947.3 16770 17130 56 2 +
MN908947.3 17087 17430 57 1 +
MN908947.3 17406 17738 58 2 +
MN908947.3 17697 18036 59 1 +
MN908947.3 17993 18324 60 2 +
MN908947.3 18275 18650 61 1 +
MN908947.3 18618 18957 62 2 +
MN908947.3 18918 19275 63 1 +
MN908947.3 19232 19591 64 2 +
MN908947.3 19570 19911 65 1 +
MN908947.3 19866 20231 66 2 +
MN908947.3 20200 20542 67 1 +
MN908947.3 20496 20867 68 2 +
MN908947.3 20813 21146 69 1 +
MN908947.3 21104 21427 70 2 +
MN908947.3 21386 21716 71 1 +
MN908947.3 21682 22013 72 2 +
MN908947.3 21990 22324 73 1 +
MN908947.3 22290 22626 74 2 +
MN908947.3 22542 22877 75 1 +
MN908947.3 22819 23192 76 2 +
MN908947.3 23144 23500 77 1 +
MN908947.3 23466 23822 78 2 +
MN908947.3 23812 24145 79 1 +
MN908947.3 24100 24443 80 2 +
MN908947.3 24416 24765 81 1 +
MN908947.3 24721 25052 82 2 +
MN908947.3 25003 25347 83 1 +
MN908947.3 25301 25646 84 2 +
MN908947.3 25623 25969 85 1 +
MN908947.3 25924 26290 86 2 +
MN908947.3 26219 26566 87 1 +
MN908947.3 26542 26890 88 2 +
MN908947.3 26857 27202 89 1 +
MN908947.3 27164 27511 90 2 +
MN908947.3 27471 27825 91 1 +
MN908947.3 27808 28145 92 2 +
MN908947.3 28104 28442 93 1 +
MN908947.3 28416 28756 94 2 +
MN908947.3 28699 29041 95 1 +
MN908947.3 29007 29356 96 2 +
MN908947.3 29316 29665 97 1 +
MN908947.3 29510 29836 98 2 +
98 changes: 98 additions & 0 deletions SARS-CoV-2/V2/nCoV-2019.insert.bed
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,98 @@
MN908947.3 54 385 1 1 +
MN908947.3 342 704 2 2 +
MN908947.3 664 1004 3 1 +
MN908947.3 965 1312 4 2 +
MN908947.3 1264 1623 5 1 +
MN908947.3 1595 1942 6 2 +
MN908947.3 1897 2247 7 1 +
MN908947.3 2205 2568 8 2 +
MN908947.3 2529 2882 9 1 +
MN908947.3 2850 3183 10 2 +
MN908947.3 3166 3507 11 1 +
MN908947.3 3482 3826 12 2 +
MN908947.3 3795 4142 13 1 +
MN908947.3 4077 4428 14 2 +
MN908947.3 4321 4674 15 1 +
MN908947.3 4658 4995 16 2 +
MN908947.3 4966 5296 17 1 +
MN908947.3 5287 5620 18 2 +
MN908947.3 5586 5932 19 1 +
MN908947.3 5894 6247 20 2 +
MN908947.3 6196 6528 21 1 +
MN908947.3 6495 6846 22 2 +
MN908947.3 6745 7092 23 1 +
MN908947.3 7058 7389 24 2 +
MN908947.3 7332 7671 25 1 +
MN908947.3 7651 7997 26 2 +
MN908947.3 7968 8319 27 1 +
MN908947.3 8275 8635 28 2 +
MN908947.3 8619 8954 29 1 +
MN908947.3 8913 9245 30 2 +
MN908947.3 9226 9557 31 1 +
MN908947.3 9502 9834 32 2 +
MN908947.3 9806 10146 33 1 +
MN908947.3 10099 10437 34 2 +
MN908947.3 10384 10737 35 1 +
MN908947.3 10688 11048 36 2 +
MN908947.3 11022 11372 37 1 +
MN908947.3 11331 11668 38 2 +
MN908947.3 11584 11927 39 1 +
MN908947.3 11889 12234 40 2 +
MN908947.3 12133 12465 41 1 +
MN908947.3 12439 12779 42 2 +
MN908947.3 12732 13074 43 1 +
MN908947.3 13027 13378 44 2 +
MN908947.3 13344 13669 45 1 +
MN908947.3 13621 13962 46 2 +
MN908947.3 13946 14271 47 1 +
MN908947.3 14232 14579 48 2 +
MN908947.3 14570 14898 49 1 +
MN908947.3 14895 15224 50 2 +
MN908947.3 15193 15538 51 1 +
MN908947.3 15503 15861 52 2 +
MN908947.3 15851 16186 53 1 +
MN908947.3 16144 16485 54 2 +
MN908947.3 16444 16804 55 1 +
MN908947.3 16770 17130 56 2 +
MN908947.3 17087 17430 57 1 +
MN908947.3 17406 17738 58 2 +
MN908947.3 17697 18036 59 1 +
MN908947.3 17993 18324 60 2 +
MN908947.3 18275 18650 61 1 +
MN908947.3 18618 18957 62 2 +
MN908947.3 18918 19275 63 1 +
MN908947.3 19232 19591 64 2 +
MN908947.3 19570 19911 65 1 +
MN908947.3 19866 20231 66 2 +
MN908947.3 20200 20542 67 1 +
MN908947.3 20496 20867 68 2 +
MN908947.3 20813 21146 69 1 +
MN908947.3 21104 21427 70 2 +
MN908947.3 21386 21716 71 1 +
MN908947.3 21682 22013 72 2 +
MN908947.3 21990 22324 73 1 +
MN908947.3 22290 22626 74 2 +
MN908947.3 22542 22877 75 1 +
MN908947.3 22819 23192 76 2 +
MN908947.3 23144 23500 77 1 +
MN908947.3 23466 23822 78 2 +
MN908947.3 23812 24145 79 1 +
MN908947.3 24100 24443 80 2 +
MN908947.3 24416 24765 81 1 +
MN908947.3 24721 25052 82 2 +
MN908947.3 25003 25347 83 1 +
MN908947.3 25301 25646 84 2 +
MN908947.3 25623 25969 85 1 +
MN908947.3 25924 26290 86 2 +
MN908947.3 26219 26566 87 1 +
MN908947.3 26542 26890 88 2 +
MN908947.3 26857 27202 89 1 +
MN908947.3 27164 27511 90 2 +
MN908947.3 27471 27825 91 1 +
MN908947.3 27808 28145 92 2 +
MN908947.3 28104 28442 93 1 +
MN908947.3 28416 28756 94 2 +
MN908947.3 28699 29041 95 1 +
MN908947.3 29007 29356 96 2 +
MN908947.3 29316 29665 97 1 +
MN908947.3 29510 29836 98 2 +
Loading

0 comments on commit 160a1db

Please sign in to comment.