Mercurial > repos > jpayne > seqsero_v2
comparison SeqSero2/SalmID/README.md @ 12:4ac593d4b40f
planemo upload
| author | jpayne |
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| date | Wed, 14 Aug 2019 17:45:41 -0400 |
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| 11:f6f0702de3b4 | 12:4ac593d4b40f |
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| 1 [](https://zenodo.org/badge/latestdoi/97020646) | |
| 2 | |
| 3 # SalmID | |
| 4 Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia). | |
| 5 | |
| 6 ## Requirements: | |
| 7 Python 3 | |
| 8 | |
| 9 ## Installation: | |
| 10 The easy way with homebrew ([Linux](http://linuxbrew.sh/) or [MacOS](https://brew.sh/)): | |
| 11 ``` | |
| 12 brew install brewsci/bio/salmid | |
| 13 ``` | |
| 14 Big thanks to [Torsten Seemann](https://tseemann.github.io/) for including this in homebrew! | |
| 15 | |
| 16 Alernatively git clone to your machine: | |
| 17 ``` | |
| 18 git clone --recursive https://github.com/hcdenbakker/SalmID.git | |
| 19 ``` | |
| 20 | |
| 21 Make SalmID executable: | |
| 22 ``` | |
| 23 cd SalmID | |
| 24 ``` | |
| 25 | |
| 26 ``` | |
| 27 chmod +x SalmID.py | |
| 28 ``` | |
| 29 | |
| 30 | |
| 31 Add the SalmID folder to your path | |
| 32 | |
| 33 To execute: | |
| 34 ``` | |
| 35 SalmID.py -e .fastq.gz | |
| 36 ``` | |
| 37 This will perform a SalmID run on all fastq.gz files in the current directory. | |
| 38 ``` | |
| 39 SalmID.py -i your_fastq_gz.fastq.gz | |
| 40 ``` | |
| 41 This will perform a SalmID run on an individual file (i.e., your_fastq_gz.fastq.gz) | |
| 42 ``` | |
| 43 SalmID.py -d directory_with_data -e _1.fastq.gz | |
| 44 ``` | |
| 45 This will perform a SalmID run on all files in directory 'directory_with_data' with extension '_1.fastq.gz' | |
| 46 | |
| 47 ## Todo's and thoughts for future releases: | |
| 48 - Provide coverage estimates for genomes in sample based on kmer frequencies | |
| 49 - Write code to use SalmID on long read (minion, pacbio) platforms |