https://github.com/lanl/adscodex
ADS Codex is a codec for organic molecular archives.
https://github.com/lanl/adscodex
Last synced: about 1 year ago
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ADS Codex is a codec for organic molecular archives.
- Host: GitHub
- URL: https://github.com/lanl/adscodex
- Owner: lanl
- License: other
- Created: 2020-04-24T12:54:51.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2023-03-09T21:00:52.000Z (over 3 years ago)
- Last Synced: 2024-06-27T00:19:26.576Z (almost 2 years ago)
- Language: Go
- Homepage:
- Size: 44.7 MB
- Stars: 33
- Watchers: 9
- Forks: 7
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-dna-storage - adscodex
README
# Adaptive DNA Storage Codec (ADS Codex)
ADS Codex is a DNA storage codec that provides high density and can adapt
to different requirements for DNA synthesis and sequencing.
## External Dependencies
### Reed-Solomon Package
ADS Codex depends on https://github.com/klauspost/reedsolomon
Please install it using
```bash
go get -u github.com/klauspost/reedsolomon
```
### Lookup Tables
Lookup tables speed up significantly ADS Codex. You can generate them
using the tblgen tool (see below), or download them from github (1.7
GB file):
https://github.com/lanl/adscodex/releases/download/1.0/tables.zip
Unpack the zip into the tbl directory where the tools and the unit
tests are expectin the lookup tables.
## Installation
To get ADS Codex clone this repository and build the packages and commands
that you are interested in. The description in
docs/howtos/HOWTO-setup-go-and-adscodex.txt has more detailed
information on how to build it.
## Documentation
The specification of the codec is located in the slides located in the
doc directory. More documentation on the implementation is located in
the source code.
The HOWTO documents in docs/howtos have more information on how to
encode and decode data with ADS Codex.
## Packages
### oligo
Contains the basic abstraction of an oligo that is used by the rest of
the packages.
### oligo/short
An implementation of the basic oligo interface that stores an oligo in
a 64-bit integer, and therefore can handle short oligos (up to 32 nts).
### oligo/long
An implementation of the basic oligo interface that can store an
arbitrary long oligo. It uses one byte per nt.
### criteria
Abstract interface for oligo viability criteria. It is used by the
Level 0 codec (l0) to check if an oligo can be synthesized/sequenced.
The package implements a single criteria: H4G2 that prevents oligos
with homopolymers longer than 4 nts (for A, T, and C) or 2 nts for G.
### l0
Level 0 of the ADS Codex codec (bit packing). Theoretically it can pack
any value up to 64 bits. In practice it is prohibitively slow to pack
large values and requires lookup tables even for 17 bit values to
achieve reasonable performance.
### l1
Level 1 of the ADS Codex codec. Packs an address and array of bytes into a
single oligo.
### l2
Level 2 of the ADS Codex codec. Packs an arbitrary array of bytes into a
collection of oligos. Provides erasure code oligos for recove of the
data in case of errors.
## Tools
The tools in the repository use the packages to provide some
convenient commands.
### tblgen
Generates encoding and decoding lookup tables for speeding-up the
Level 0 encoding and decoding.
For example, generating an encoding lookup table for 17 nts oligos
that has 2^13 entries can be done by:
```bash
./tblgen -e encnt17b13.tbl -l 17 -b 13
```
Generating a decoding lookup table for 17 nts oligos that has 2^14
entries can be done by:
```bash
./tblgen -d decnt17b7.tbl -l 17 -b 7
```
Although the code is parallelized and uses all available cores, it can
take few hours to generate the table.
### encode
Encodes the specified file and outputs a list of oligos that represent
it.
### decode
Decodes the specified list of oligos into a file. If not all data can
be recovered, the output file might have holes.
### Miscelaneous utilities
The utils directory contains many utilities that can be used to
analyze sequenced data.
## Unit Tests
The packages have some limited unit tests that can be run by the
standard:
```bash
go test
```
The unit tests will slowly be extended to cover all use cases.
## Limitations
There are multiple TODO and FIXME comments in the source code that
describe things that are missing, or implementation restrictions that
should be fixed eventually.