Readme

README.md

@@ -2,44 +2,72 @@
 
 # Hostile
 
-Rapid FASTQ decontamination by host depletion. Accepts paired fastq.gz files as arguments and outputs paired fastq.gz files. Downloads and caches a custom human reference genome to `$XDG_DATA_DIR`. Replaces read headers with incrementing integers for speed and privacy. Python package with CLI and Python API. Installs with conda/mamba.
+Rapid FASTQ decontamination by host subtraction. Accepts Illumina or ONT fastq[.gz] input and outputs fastq.gz files. Downloads and caches a custom human T2T + HLA reference genome to `$XDG_DATA_DIR` when run for the first time. Replaces read headers with incrementing integers for speed and privacy. Python package with CLI and Python API. Installs with conda/mamba. Please read the [BioRxiv preprint](https://www.biorxiv.org/content/10.1101/2023.07.04.547735) for further information, and open a GitHub issue if you encounter problems.
 
 
 
 ## Install
 
+### Conda
+
+```bash
+curl -OJ https://raw.githubusercontent.com/bede/hostile/main/environment.yml
+conda env create -f environment.yml  # Mamba is faster
+conda activate hostile
+pip install hostile
+
+# Test
+hostile clean --fastq1 tests/data/mixed_human_100_1.fastq.gz --fastq2 tests/data/mixed_human_100_2.fastq.gz
+```
+
+
+
+### Docker
+
+*Coming soon*
+
+
+
+### Development install
+
 ```bash
 git clone https://github.com/bede/hostile.git
 cd hostile
 conda env create -f environment.yml  # Use mamba if impatient
 conda activate hostile
-pip install .
+pip install --editable '.[dev]'
+pytest
 ```
 
 
 
+
 ## Command line usage
 
 ```bash
 % hostile clean --help
-usage: hostile clean [-h] --fastq1 FASTQ1 --fastq2 FASTQ2 [--aligner {bowtie2,minimap2}] [--out-dir OUT_DIR] [--threads THREADS] [--debug]
+usage: hostile clean [-h] --fastq1 FASTQ1 [--fastq2 FASTQ2] [--aligner {bowtie2,minimap2}] [--custom-index CUSTOM_INDEX] [--out-dir OUT_DIR]
+                     [--threads THREADS] [--debug]
 
-Remove human reads from paired fastq.gz files
+Remove human reads from paired fastq(.gz) files
 
 options:
   -h, --help            show this help message and exit
-  --fastq1 FASTQ1       path to forward fastq.gz file
-  --fastq2 FASTQ2       path to reverse fastq.gz file
+  --fastq1 FASTQ1       path to forward fastq(.gz) file
+  --fastq2 FASTQ2       optional path to reverse fastq(.gz) file
+                        (default: None)
   --aligner {bowtie2,minimap2}
                         alignment algorithm
                         (default: bowtie2)
+  --custom-index CUSTOM_INDEX
+                        path to custom index
+                        (default: None)
   --out-dir OUT_DIR     output directory for decontaminated fastq.gz files
-                        (default: /Users/bede/Research/Git/hostile)
+                        (default: /root/hostile/tests/data)
   --threads THREADS     number of CPU threads to use
-                        (default: 10)
+                        (default: 1)
   --debug               show debug messages
-                        (default: False)
-
+                        (default: False)       (default: False)
 ```
 
 
@@ -64,28 +92,19 @@ Cleaning: 100%|█████████████████████
         "reads_removed_proportion": 0.0
     }
 ]
-
 ```
 
 
 
 ## Python usage
 
 ```python
+from pathlib import Path
 from hostile.lib import clean_paired_fastqs
 
-decontamination_statistics = clean_paired_fastqs(fastqs=[("h37rv_10.r1.fastq.gz", fastq2="h37rv_10.r1.fastq.gz")])
-```
-
-
-
-## Development
+stats = clean_paired_fastqs(
+    fastqs=[(Path("h37rv_10.r1.fastq.gz"), Path("h37rv_10.r1.fastq.gz"))]
+)
 
-```bash
-git clone https://github.com/bede/hostile.git
-cd hostile
-conda env create -f environment.yml  # Use mamba if impatient
-conda activate hostile
-pip install --editable '.[dev]'
-pytest
+print(stats)
 ```