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- ipynbsadd ipynb for how taxonomy info was retreived8年前
- refseq_masherFix setup.py so that package can be correctly built for pypi5年前
- testsChecking log for message string.5年前
- .gitignore.8年前
- .travis.ymladd ipynb for how taxonomy info was retreived8年前
- LICENSEinit commit8年前
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- NOTICEinit commit8年前
- README.mdUpdate README8年前
- setup.pyFix setup.py so that package can be correctly built for pypi5年前
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版权所有：中国计算机学会技术支持：开源发展技术委员会
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RefSeq Masher
Find what NCBI RefSeq genomes match or are contained within your sequence data using Mash MinHash with a Mash sketch database of 54,925 NCBI RefSeq Genomes.
Installation
Easiest way to install
refseq_masherand all its dependencies is with Conda through the BioConda channel:Otherwise you can install
refseq_masherfrom PyPI withpip install refseq_masher, but you would need to manually install Mash v2.0+.Dependencies
Other than Python 3.5/3.6, the only external dependency of
refseq_masheris Mash v2.0+.Python dependencies
Usage
If you run
refseq_masherwithout any arguments, you should see the following usage info:refseq_masherhas 2 commands:matchesfor finding the closest NCBI RefSeq genome matches to your input sequencescontainsfor finding what RefSeq genomes are contained within your input sequencesmatches- find the closest matching NCBI RefSeq Genomes in your input sequencesExample
With the FNA.GZ file for Salmonella enterica subsp. enterica serovar Enteritidis str. CHS44:
Log:
Output:
Table output to standard output:
The top match is Salmonella enterica subsp. enterica serovar Enteritidis str. CHS44 with a distance of 0.0 and 400/400 sketches matching, which is what we expected. There’s other taxonomic information available in the results table that may be useful.
contains- find what NCBI RefSeq Genomes are contained in your input sequencesIf you have a metagenomic sample or maybe a sample with some contamination, you may be interested in seeing what’s in your sample. You can do this with
refseq_masher contains <INPUT>.Example - metagenomic a sample SAMEA1877339
For this example, we’re going to see what RefSeq genomes are contained within sample SAMEA1877340 from BioProject PRJEB1775.
Description from BioProject PRJEB1775:
We’re going to download the FASTQ files for ERR260489:
We’re going to run
refseq_masheragainst these FASTQ files:Log:
Output:
Some of the top genomes contained in this sample are sorted by identity and median multiplicity are:
So with Mash we are able to find that the sample contained the expected genomic data (especially E. coli O104:H4).
Legal
Copyright Government of Canada 2017
Written by: National Microbiology Laboratory, Public Health Agency of Canada
Licensed under the Apache License, Version 2.0 (the “License”); you may not use this work except in compliance with the License. You may obtain a copy of the License at:
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Contact
Gary van Domselaar: gary.vandomselaar@phac-aspc.gc.ca