Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains.
Project description
StrainGE: Strain-level Genome Exploration
StrainGE is a set of tools to analyse the within-species strain diversity in bacterial populations. It consists of two main components: 1) StrainGST: Strain Genome Search tool, a tool to find close reference genomes for strains present in a sample and 2) StrainGR: Strain Genome Recovery, a tool to perform strain-aware variant calling at low coverages.
Dependencies
Python packages
- Python >= 3.7
- NumPy
- SciPy
- matplotlib
- scikit-bio >= 0.5
- scikit-learn >= 0.24
- pyvcf
- pysam
- h5py
- intervaltree
Bioinformatics tools
- bwa
- samtools
- mummer
Installation
Python Package Index
pip install strainge
You'll have to make sure all tools like bwa
, samtools
and mummer
are installed as well.
Conda
-
Install Anaconda or miniconda (if not already present on your system)
-
Clone the repository:
git clone https://github.com/broadinstitute/StrainGE
-
Move into the directory:
cd StrainGE
-
Create a new conda environment:
conda env create -f environment.yml
-
Activate the environment:
source activate strainge
Documentation
The documentation can be read on readthedocs.
Citation
Dijk LR van, Walker BJ, Straub TJ, Worby C, Grote A, Schreiber HL, et al. StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities. bioRxiv. 2021 Feb 14;2021.02.14.431013.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distributions
Hashes for strainge-1.1.4-pp37-pypy37_pp73-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 65f297cb7b76cc498c6108f96c0f5e7262bab426d41980e3a05cb2e2c2a459ea |
|
MD5 | 6bc5cdf1f495f428528c05f5c7105d05 |
|
BLAKE2b-256 | 8f5bd2829a84288c0f4f72b499e452a530c528ec27149fe06a450e465131c2d1 |
Hashes for strainge-1.1.4-pp37-pypy37_pp73-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 7515e4a0333ee2ff171620c8f0eff9d39b0b84253b3aa6bb1a2cc61bb31e3fe0 |
|
MD5 | 8a5c01431fb536f594b21c8dd4d0b443 |
|
BLAKE2b-256 | 35914b6bef6db22e9c1b278b93c7d39c2c3fedec3c369d8976b7a57c2ac0c7c3 |
Hashes for strainge-1.1.4-cp39-cp39-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | f4ceb77b79cff38e6f370e5254a0d5dc537bb956fa1e79b9c63eaff2da9606c9 |
|
MD5 | aa251f4169167402d266bbc66fde8a3a |
|
BLAKE2b-256 | 1454717591fc78b08001b691dd51cd3fae3b535ab23f34930d67d21f17cdfa87 |
Hashes for strainge-1.1.4-cp39-cp39-manylinux2010_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 845e0cbbcbbebb88afd69224cf6e4f7f08dc9b682c6a9176a4e4dc1e93d0dc41 |
|
MD5 | bac41e0971d66d36d6964953e74af252 |
|
BLAKE2b-256 | 63911736e8625b6ce076c253eeeb8789b8dd8ee827427ef65099699405ada8e1 |
Hashes for strainge-1.1.4-cp39-cp39-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | fa0ddc28b32268b186fb88ca213ea5e727c29f6d7f826bd4a73e93abb5867330 |
|
MD5 | ac36b7d9f8c46fef88f52c118de9c707 |
|
BLAKE2b-256 | 28d4f291f3d5070f1b63babc57e1d9ffa6e4ff1488c2951a83fc14e577274d0b |
Hashes for strainge-1.1.4-cp38-cp38-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 81449d9665d5adca18911f6f3df80bf8ee8fd9ceaee6d56b8d15b0bb448b3b16 |
|
MD5 | dc350a23e463964e32d86bdebb4db587 |
|
BLAKE2b-256 | dd92769ea3e7e7349ce4d6deb299954282a09f9430124e254f79294db8850dbc |
Hashes for strainge-1.1.4-cp38-cp38-manylinux2010_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 0753616a6a255d3314fc11ceabc3835d9b743002df5eb3743d41c17340c010f7 |
|
MD5 | 0e914ef9dff9a322e7028509f2cf6106 |
|
BLAKE2b-256 | 01f03b410419fc09f0a0a7e767d4a0e112d6ec18e61a82481c972185ff84e009 |
Hashes for strainge-1.1.4-cp38-cp38-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | eb839af2a3029efdaa9811ebb1fe934e3216213077da3e3bdffe94fd63a00c01 |
|
MD5 | 8ea8e489c52aa326ed7d913f7d7df511 |
|
BLAKE2b-256 | a1aaf7b8d4aa5814581f06ce841ab8eab3c362a8f158ffe671c5b8fcc514fbe3 |
Hashes for strainge-1.1.4-cp37-cp37m-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c87ff54ae0fdd08fcb99ba91f828994bd2d1ccf32eb7a92e3a950965fa8e0c0f |
|
MD5 | eacc3bc5e536243d1b215eeb39522cbe |
|
BLAKE2b-256 | 5bdadf752dc7dee2e0c7620b860b25b3050dd1788d0d4399b9130cc46b7eba16 |
Hashes for strainge-1.1.4-cp37-cp37m-manylinux2010_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | afd8ad83a7318bd368e4d85b490cc222dbda55c32eda35d14561c306416c17c5 |
|
MD5 | 0dea938d614d3f7ffc155bc10d20100e |
|
BLAKE2b-256 | a36d53eac936b0cad2f49fd59d18cf29e6e846b406c0d50eaaa80417a6733ce2 |
Hashes for strainge-1.1.4-cp37-cp37m-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 461ecf8b418c9357037937553a8b174293a1571d6f9bedb7c75fddb246288ee3 |
|
MD5 | 76764f3c0c2207e559ba9bcf551bf1c6 |
|
BLAKE2b-256 | 4e8aa4c10fabd7092e94e239bbc168baed0275ffc5fd3ccba5348ef9ed720ccb |