|
1 | 1 | # Software that supports S/BLOW5 |
2 | 2 |
|
3 | | -^ developed by us |
4 | | -> a fork managed by us |
5 | | -< contributed by us as a pull request |
6 | | -* developed by others |
| 3 | +⚡developed by us </br> |
| 4 | +🔀a fork managed by us </br> |
| 5 | +🔼contributed by us as a pull request </br> |
| 6 | +🌟developed by others </br> |
7 | 7 |
|
8 | 8 | ## Basecalling |
9 | 9 |
|
10 | | -- ^[buttery-eel](https://github.com/Psy-Fer/buttery-eel) for Guppy/Dorado server |
11 | | -- >[slow5-dorado](https://github.com/hiruna72/slow5-dorado/releases) (fork of Dorado) |
12 | | -- >Bonito (through our [fork](https://github.com/Psy-Fer/bonito)) |
13 | | -- ^[slorado](https://github.com/BonsonW/slorado) |
14 | | -- <[RODAN](https://github.com/biodlab/RODAN/pull/6) |
15 | | -- <[radian](https://github.com/comprna/radian/pull/5) |
| 10 | +- [buttery-eel](https://github.com/Psy-Fer/buttery-eel) for Guppy/Dorado server⚡ |
| 11 | +- [slow5-dorado](https://github.com/hiruna72/slow5-dorado/releases) (fork of Dorado)🔀 |
| 12 | +- Bonito (through our [fork](https://github.com/Psy-Fer/bonito))🔀 |
| 13 | +- [slorado](https://github.com/BonsonW/slorado)⚡ |
| 14 | +- [RODAN](https://github.com/biodlab/RODAN/pull/6)🔼 |
| 15 | +- [radian](https://github.com/comprna/radian/pull/5)🔼 |
16 | 16 |
|
17 | 17 | ## Methylation calling |
18 | 18 |
|
19 | | -- ^[buttery-eel](https://github.com/Psy-Fer/buttery-eel/) for running remora models through Guppy/Dorado server |
20 | | -- >[slow5-dorado](https://github.com/hiruna72/slow5-dorado/releases) (fork of Dorado) |
21 | | -- ^[f5c](https://github.com/hasindu2008/f5c/) (version 0.8 onwards) |
22 | | -- <[nanopolish](https://github.com/jts/nanopolish) (version 0.14.0 onwards) |
| 19 | +- [buttery-eel](https://github.com/Psy-Fer/buttery-eel/) for running remora models through Guppy/Dorado server⚡ |
| 20 | +- [slow5-dorado](https://github.com/hiruna72/slow5-dorado/releases) (fork of Dorado)🔀 |
| 21 | +- [f5c](https://github.com/hasindu2008/f5c/) (version 0.8 onwards)⚡ |
| 22 | +- [nanopolish](https://github.com/jts/nanopolish) (version 0.14.0 onwards)🔼 |
23 | 23 |
|
24 | 24 | ## raw signal mapping/alignment |
25 | 25 |
|
26 | | -- <[sigmap](https://github.com/haowenz/sigmap) |
27 | | -- <[OpenDBA](https://github.com/nodrogluap/OpenDBA) |
28 | | -- ^[sigfish](https://github.com/beebdev/sigfish) and [HARU](https://github.com/beebdev/HARU) |
29 | | -- ^[DeepSelectNet](https://github.com/AnjanaSenanayake/DeepSelectNet) |
30 | | -- <[SquiggleNet](https://github.com/welch-lab/SquiggleNet/pull/6) |
31 | | -- *[RawHash](https://github.com/CMU-SAFARI/RawHash/) |
32 | | -- *[UNCALLED4](https://github.com/skovaka/uncalled4) |
| 26 | +- [sigmap](https://github.com/haowenz/sigmap)🔼 |
| 27 | +- [OpenDBA](https://github.com/nodrogluap/OpenDBA)🔼 |
| 28 | +- [sigfish](https://github.com/beebdev/sigfish) and [HARU](https://github.com/beebdev/HARU)⚡ |
| 29 | +- [DeepSelectNet](https://github.com/AnjanaSenanayake/DeepSelectNet)⚡ |
| 30 | +- [SquiggleNet](https://github.com/welch-lab/SquiggleNet/pull/6)🔼 |
| 31 | +- [RawHash](https://github.com/CMU-SAFARI/RawHash/)🌟 |
| 32 | +- [UNCALLED4](https://github.com/skovaka/uncalled4)🌟 |
33 | 33 |
|
34 | 34 | ## raw signal manipulation |
35 | 35 |
|
36 | | -- ^[sigtk](https://github.com/hasindu2008/sigtk) |
37 | | -- ^[slow5tools](https://github.com/hasindu2008/slow5tools) |
38 | | -- ^[slow5curl](https://github.com/BonsonW/slow5curl) |
| 36 | +- [sigtk](https://github.com/hasindu2008/sigtk)⚡ |
| 37 | +- [slow5tools](https://github.com/hasindu2008/slow5tools)⚡ |
| 38 | +- [slow5curl](https://github.com/BonsonW/slow5curl)⚡ |
39 | 39 |
|
40 | 40 | ## conversion |
41 | 41 |
|
42 | | -- ^[slow5tools](https://github.com/hasindu2008/slow5tools) |
43 | | -- ^[blue-crab](https://github.com/Psy-Fer/blue-crab) |
| 42 | +- [slow5tools](https://github.com/hasindu2008/slow5tools)⚡ |
| 43 | +- [blue-crab](https://github.com/Psy-Fer/blue-crab)⚡ |
44 | 44 |
|
45 | 45 | ## raw signal simulation |
46 | 46 |
|
47 | | -- ^[squigulator](https://github.com/hasindu2008/squigulator/) |
| 47 | +- [squigulator](https://github.com/hasindu2008/squigulator/)⚡ |
| 48 | +- [seq2squiggle](https://github.com/ZKI-PH-ImageAnalysis/seq2squiggle)🌟 |
48 | 49 |
|
49 | 50 | ## raw signal visualisation |
50 | 51 |
|
51 | | -- ^[squigualiser](https://github.com/hiruna72/squigualiser) |
52 | | -- *[nanoCEM](https://github.com/lrslab/nanoCEM) |
| 52 | +- [squigualiser](https://github.com/hiruna72/squigualiser)⚡ |
| 53 | +- [nanoCEM](https://github.com/lrslab/nanoCEM)🌟 |
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