3 changes

README.md

@@ -1,2 +1,70 @@
-# pima
+# **pima**
 Plasmid and antimicrobial resistance pipeline
+
+### Example Installation
+Pima is not yet packaged, but its primary dependencies are _mostly_ available. `guppy` must be manually installed with info [here](https://nanoporetech.com/community). If you don't yet have `conda` installed you'll need to do that [here](https://docs.anaconda.com/anaconda/install/). Once installed you can create an environment where `pima.py` will run.
+```sh
+conda create -n pima_env2 python=2.7.16
+source activate pima_env2
+# install python modules
+conda install -c conda-forge joblib numpy pandas pathos -y
+# install bioinfx packages
+conda install -c bioconda bcftools bedtools blast flye mummer medaka miniasm minimap2 nanopolish parallel porechop qcat racon samtools spades wtdbg -y
+git clone https://github.com/abconley/pima.git $HOME
+python ~/pima/pima.py --help
+```
+
+##### Compatibility
+Currently several unix utilities are used, so this is not compatible with Windows OS. CentOS and Ubuntu are both known working OSes.
+
+
+
+##### Dependencies
+| System Command | Package |
+| -------------- | ------- |
+| `bcftools` | BCFtools |
+| `bedtools` | BEDTools |
+| `blastn` | BLAST+ |
+| `dnadiff` | MUMmer |
+| `faidx` | SAMtools |
+| `flye` | Flye |
+| `parallel` | GNU parallel |
+| `guppy_basecaller` | Guppy |
+| `makeblastdb` | BLAST+ |
+| `medaka_consensus` | Medaka |
+| `miniasm` | miniasm |
+| `minimap2` | minimap2 |
+| `nanopolish` | Nanopolish |
+| `nanopolish_makerange.py` | Nanopolish |
+| `pblat` | pblat |
+| `pChunks.R` | local R script |
+| `porechop` | Porechop |
+| `qcat` | Qcat |
+| `racon` | racon |
+| `read_fast5_basecaller.py` | Guppy |
+| `samtools` | SAMtools |
+| `spades.py` | SPAdes |
+| `wtdbg2` | Wtdbg2 |
+| `wtpoa-cns` | Wtdbg2 |
+|  |  |
+| `awk` | Unix |
+| `cat` | Unix |
+| `grep` | Unix |
+| `head` | Unix |
+| `ls` | Unix |
+| `sed` | Unix |
+| `sort` | Unix |
+
+#### Literature Citations
+- McLaughlin HP, Bugrysheva JV, Conley AB, Gulvik CA, Kolton CB, Marston C, Swaney E, Lonsway DR, Cherney B, Gargis AS, Kongphet-Tran T, Lascols C, Michel P, Villanueva J, Hoffmaster ER, Gee JE, Sue D. 2020. When minutes matter: rapid nanopore whole genome sequencing for anthrax emergency preparedness. Emerging Infectious Diseases
+- [BCFtools and SAMtools](https://www.ncbi.nlm.nih.gov/pubmed/19505943)
+- [BEDTools](https://www.ncbi.nlm.nih.gov/pubmed/25199790)
+- [BLAST+](https://www.ncbi.nlm.nih.gov/pubmed/20003500)
+- [GNU parallel](https://www.usenix.org/publications/login/february-2011-volume-36-number-1/gnu-parallel-command-line-power-tool)
+- [Flye](https://www.ncbi.nlm.nih.gov/pubmed/30936562)
+- [miniasm and minimap2](https://www.ncbi.nlm.nih.gov/pubmed/27153593)
+- [MUMmer](https://www.ncbi.nlm.nih.gov/pubmed/14759262)
+- [pblat](https://www.ncbi.nlm.nih.gov/pubmed/30646844)
+- [racon](https://www.ncbi.nlm.nih.gov/pubmed/28100585)
+- [SPAdes](https://www.ncbi.nlm.nih.gov/pubmed/22506599)
+- [Wtdbg2](https://www.nature.com/articles/s41592-019-0669-3)