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0.3.0
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bede committed Nov 22, 2023
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29 changes: 18 additions & 11 deletions README.md
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Expand Up @@ -36,7 +36,7 @@ conda activate hostile
**Docker**

```bash
docker run quay.io/biocontainers/hostile:0.1.0--pyhdfd78af_0
docker run quay.io/biocontainers/hostile:0.2.0--pyhdfd78af_0

# Build your own
wget https://raw.githubusercontent.com/bede/hostile/main/Dockerfile
Expand All @@ -62,31 +62,36 @@ pytest

```bash
$ hostile clean --help
usage: hostile clean [-h] --fastq1 FASTQ1 [--fastq2 FASTQ2] [--aligner {bowtie2,minimap2,auto}] [--index INDEX] [--rename] [--out-dir OUT_DIR] [--threads THREADS] [--force] [--debug]
usage: hostile clean [-h] --fastq1 FASTQ1 [--fastq2 FASTQ2] [--aligner {bowtie2,minimap2,auto}] [--index INDEX] [--rename] [--sort-by-name] [--out-dir OUT_DIR] [--threads THREADS]
[--aligner-args ALIGNER_ARGS] [--force] [--debug]

Remove host reads from paired fastq(.gz) files
Remove reads aligning to a target genome from fastq[.gz] input files

options:
-h, --help show this help message and exit
--fastq1 FASTQ1 path to forward fastq(.gz) file
--fastq2 FASTQ2 optional 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,auto}
alignment algorithm
alignment algorithm. Use Bowtie2 for short reads and Minimap2 for long reads
(default: auto)
--index INDEX path to custom genome or index. For Bowtie2, provide an index path without the .bt2 extension
--index INDEX path to custom genome or index. For Bowtie2, provide an index without .bt2 extension
(default: None)
--rename replace read names with incrementing integers
(default: False)
--sort-by-name sort reads by name (before renaming, if enabled)
(default: False)
--out-dir OUT_DIR path to output directory
(default: ./)
--threads THREADS number of CPU threads to use
(default: /Users/bede/Research/Git/hostile)
--threads THREADS number of threads to use
(default: 10)
--aligner-args ALIGNER_ARGS
additional arguments for alignment
(default: )
--force overwrite existing output files
(default: False)
--debug show debug messages
(default: False)

```
Expand Down Expand Up @@ -199,7 +204,9 @@ hostile clean --index masked-index --fastq1 reads_1.fastq.gz --fastq2 reads_2.fa

## Citation

```
[BioRxiv preprint](https://www.biorxiv.org/content/10.1101/2023.07.04.547735) (accepted for publication in Oxford Bioinformatics)

```latex
@article {Constantinides2023,
author = {Bede Constantinides and Martin Hunt and Derrick W Crook},
title = {Hostile: accurate host decontamination of microbial sequences},
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2 changes: 1 addition & 1 deletion src/hostile/__init__.py
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@@ -1,2 +1,2 @@
"""Accurate host read removal"""
__version__ = "0.2.0"
__version__ = "0.3.0"
2 changes: 1 addition & 1 deletion src/hostile/cli.py
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Expand Up @@ -38,7 +38,7 @@ def clean(
:arg aligner: alignment algorithm. Use Bowtie2 for short reads and Minimap2 for long reads
:arg index: path to custom genome or index. For Bowtie2, provide an index without .bt2 extension
:arg rename: replace read names with incrementing integers
:arg sort_by_name: sort reads by name
:arg sort_by_name: sort reads by name (before renaming, if enabled)
:arg out_dir: path to output directory
:arg threads: number of threads to use
:arg aligner_args: additional arguments for alignment
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