Mercurial > repos > jpayne > seqsero_v2
annotate SeqSero2/SalmID/README.md @ 13:3513b93ebe6a
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| author | jpayne |
|---|---|
| date | Tue, 03 Sep 2019 12:40:46 -0400 |
| parents | 4ac593d4b40f |
| children |
| rev | line source |
|---|---|
| jpayne@12 | 1 [](https://zenodo.org/badge/latestdoi/97020646) |
| jpayne@12 | 2 |
| jpayne@12 | 3 # SalmID |
| jpayne@12 | 4 Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia). |
| jpayne@12 | 5 |
| jpayne@12 | 6 ## Requirements: |
| jpayne@12 | 7 Python 3 |
| jpayne@12 | 8 |
| jpayne@12 | 9 ## Installation: |
| jpayne@12 | 10 The easy way with homebrew ([Linux](http://linuxbrew.sh/) or [MacOS](https://brew.sh/)): |
| jpayne@12 | 11 ``` |
| jpayne@12 | 12 brew install brewsci/bio/salmid |
| jpayne@12 | 13 ``` |
| jpayne@12 | 14 Big thanks to [Torsten Seemann](https://tseemann.github.io/) for including this in homebrew! |
| jpayne@12 | 15 |
| jpayne@12 | 16 Alernatively git clone to your machine: |
| jpayne@12 | 17 ``` |
| jpayne@12 | 18 git clone --recursive https://github.com/hcdenbakker/SalmID.git |
| jpayne@12 | 19 ``` |
| jpayne@12 | 20 |
| jpayne@12 | 21 Make SalmID executable: |
| jpayne@12 | 22 ``` |
| jpayne@12 | 23 cd SalmID |
| jpayne@12 | 24 ``` |
| jpayne@12 | 25 |
| jpayne@12 | 26 ``` |
| jpayne@12 | 27 chmod +x SalmID.py |
| jpayne@12 | 28 ``` |
| jpayne@12 | 29 |
| jpayne@12 | 30 |
| jpayne@12 | 31 Add the SalmID folder to your path |
| jpayne@12 | 32 |
| jpayne@12 | 33 To execute: |
| jpayne@12 | 34 ``` |
| jpayne@12 | 35 SalmID.py -e .fastq.gz |
| jpayne@12 | 36 ``` |
| jpayne@12 | 37 This will perform a SalmID run on all fastq.gz files in the current directory. |
| jpayne@12 | 38 ``` |
| jpayne@12 | 39 SalmID.py -i your_fastq_gz.fastq.gz |
| jpayne@12 | 40 ``` |
| jpayne@12 | 41 This will perform a SalmID run on an individual file (i.e., your_fastq_gz.fastq.gz) |
| jpayne@12 | 42 ``` |
| jpayne@12 | 43 SalmID.py -d directory_with_data -e _1.fastq.gz |
| jpayne@12 | 44 ``` |
| jpayne@12 | 45 This will perform a SalmID run on all files in directory 'directory_with_data' with extension '_1.fastq.gz' |
| jpayne@12 | 46 |
| jpayne@12 | 47 ## Todo's and thoughts for future releases: |
| jpayne@12 | 48 - Provide coverage estimates for genomes in sample based on kmer frequencies |
| jpayne@12 | 49 - Write code to use SalmID on long read (minion, pacbio) platforms |