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fastqwiper-2021.1.58
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مشاهده بیشترتوضیحات
A package to wipe out uncompliant reads from FASTQ files
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | fastqwiper-2021.1.58 |
| نام | fastqwiper |
| نسخه کتابخانه | 2021.1.58 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Tommaso Mazza |
| ایمیل نویسنده | bioinformatics@css-mendel.it |
| آدرس صفحه اصلی | https://github.com/mazzalab/fastqwiper |
| آدرس اینترنتی | https://pypi.org/project/fastqwiper/ |
| مجوز | MIT |
# FastqWiper
[](https://ci.appveyor.com/project/mazzalab/fastqwiper)
[](https://github.com/mazzalab/fastqwiper/issues)
`FastqWiper` is a Python application that wipes out badly formatted reads from readable FASTQ files.
More complex workflows, as **recover** corrupted `fastq.gz`, **dropping** or **fixing** pesky lines, **removing**
unpaired reads, and **fixing** reads interleaving, can be executed using Snakemake and the preconfigured
[pipeline files](https://github.com/mazzalab/fastqwiper/tree/main/pipeline) provided here.
* Compatibility: Python <3.9
* OS: Windows (excluding pipelines), Linux, Mac OS
* Contributions: [bioinformatics@css-mendel.it](bioinformatics@css-mendel.it)
* Pypi: https://pypi.org/project/fastqwiper
* Conda: https://anaconda.org/bfxcss/fastqwiper
* Docker Hub: available soon
* Bug report: [https://github.com/mazzalab/fastqwiper/issues](https://github.com/mazzalab/fastqwiper/issues)
## Installation
`FastqWiper` alone can be installed using both Conda and PyPi and runs smoothly on all OS specified above.
### Anaconda or Miniconda
[](https://anaconda.org/bfxcss/fastqwiper) [](https://anaconda.org/bfxcss/fastqwiper) [](https://anaconda.org/bfxcss/fastqwiper) [](https://anaconda.org/bfxcss/fastqwiper)
Create and activate an empty Conda environment, if not already available.<br/>
```
$ conda create -n FastqWiper python=3.8
$ conda activate FastqWiper
```
then<br/>
`$ conda install -y -c bfxcss -c conda-forge fastqwiper`
### Pypi
[](https://pypi.org/project/fastqwiper/)
`pip install fastqwiper`
### Usage
`fastqwiper` `<options>`
```
options:
--fastq_in TEXT The input FASTQ file to be cleaned [required]
--fastq_out TEXT The wiped FASTQ file [required]
--log_frequency INTEGER The number of processed reads that you want to print a status message after
```
It accepts in input and outputs **readable** `*.fastq` or `*.fastq.gz` files.
## Snakemake
To enable the use of preconfigured [pipelines](https://github.com/mazzalab/fastqwiper/tree/main/pipeline), you need to
install **Snakemake**. The recommended way to install Snakemake is via Conda, because it enables **Snakemake** to
[handle software dependencies of your workflow](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#integrated-package-management).
However, the default conda solver is slow and often hangs. Therefore, we recommend
installing [Mamba](https://github.com/mamba-org/mamba) as a drop-in replacement via
`$ conda install -c conda-forge mamba`
and then creating and activating a clean environment as above:
```
$ mamba create -c conda-forge -c bioconda -n FastqWiper snakemake
$ conda activate FastqWiper
$ conda install colorama click
$ conda install mamba -c conda-forge
```
### Usage
Clone the FastqWiper repository:
`git clone https://github.com/mazzalab/fastqwiper.git`.
It contains, in particular, a folder `data` containing the fastq files to be processed, a folder `pipeline` containing
the released pipelines and a folder `fastq_wiper` with the source files of FastqWiper. <br/>
Input files to be processed should be copied into the **data** folder. All software packages not fetched from `Conda`
and used by the pipelines should be copied, even if it is not strictly mandatory, in the root directory of the cloned
repository.
Currently, to run the FastqWiper pipelines, the following packages are not included in `Conda` but are
required:
### required packages:
[gzrt](https://github.com/arenn/gzrt) (install [instructions](https://github.com/arenn/gzrt/blob/master/README.build))
[BBTools](https://jgi.doe.gov/data-and-tools/bbtools/) (install [instructions](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/installation-guide/))
```
$ cd fastqwiper
$ git clone https://github.com/arenn/gzrt.git
$ cd gzrt
$ make
$ cd ..
$ cd fastqwiper
$ tar -xvzf BBMap_(version).tar.gz
```
### Commands:
#### Paired-end files
- **Personalize a pipeline**. Using `fix_wipe_pairs_reads.smk` requires you to edit
line 3 of the file with the name of the fastq files stored in `data` folder that you want to process.
If the files were:
```
excerpt_S1_R1_001.fastq.gz
excerpt_S1_R2_001.fastq.gz
sample_S1_R1_001.fastq.gz
sample_S1_R2_001.fastq.gz
```
the SAMPLE vector should be: `SAMPLES = ["sample", "excerpt"]`
- **Get a dry run** of a pipeline (e.g., `fix_wipe_pairs_reads.smk`):<br />
`snakemake -s pipeline/fix_wipe_pairs_reads.smk --use-conda --cores 2 -np`
- **Generate the planned DAG**:<br />
`snakemake -s pipeline/fix_wipe_pairs_reads.smk --dag | dot -Tpdf > dag.pdf`<br />
<img src="https://github.com/mazzalab/fastqwiper/blob/main/pipeline/fix_wipe_pairs_reads.png?raw=true" width="400">
- **Run the pipeline** (n.b., during the first execution, Snakemake will download and install some required remote
packages and may take longer). The number of computing cores can be tuned accordingly:<br />
`snakemake -s pipeline/fix_wipe_pairs_reads.smk --use-conda --cores 2`
Fixed files will be copied in the `data` folder and will be suffixed with the string `_fixed_wiped_paired_interleaving`.
We remind that the `fix_wipe_pairs_reads.smk` pipeline performs the following actions:
- execute `gzrt` on corrupted fastq.gz files (i.e., that cannot be unzipped because of errors) and recover readable reads;
- execute `fastqwiper` on recovered reads to make them compliant with the FASTQ format (source: [Wipipedia](https://en.wikipedia.org/wiki/FASTQ_format))
- execute `Trimmomatic` on wiped reads to remove residual unpaired reads
- execute `BBmap (repair.sh)` on paired reads to fix the correct interleaving and sort fastq files.
#### Single-end files
Using `fix_wipe_pairs_reads.smk` requires you to make the same edits as above. This pipeline will not execute
`trimmomatic` and BBmap's `repair.sh`.
- **Get a dry run** of a pipeline (e.g., `fix_wipe_single_reads.smk`):<br />
`snakemake -s pipeline/fix_wipe_single_reads.smk --use-conda --cores 2 -np`
- **Generate the planned DAG**:<br />
`snakemake -s pipeline/fix_wipe_single_reads.smk --dag | dot -Tpdf > dag.pdf`<br />
<img src="https://github.com/mazzalab/fastqwiper/blob/main/pipeline/fix_wipe_single_reads.png?raw=true" width="200">
- **Run the pipeline** (n.b., during the first execution, Snakemake will download and install some required remote
packages and may take longer). The number of computing cores can be tuned accordingly:<br />
`snakemake -s pipeline/fix_wipe_single_reads.smk --use-conda --cores 2`
# Author
**Tommaso Mazza**
[](https://twitter.com/irongraft)
Laboratory of Bioinformatics<br/>
Fondazione IRCCS Casa Sollievo della Sofferenza<br/>
Viale Regina Margherita 261 - 00198 Roma IT<br/>
Tel: +39 06 44160526 - Fax: +39 06 44160548<br/>
E-mail: t.mazza@css-mendel.it <br/>
Web page: http://www.css-mendel.it <br/>
Web page: http://bioinformatics.css-mendel.it <br/>
نیازمندی
| مقدار | نام |
|---|---|
| - | setuptools |
| ==0.4.4 | colorama |
| ==7.1.2 | click |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| <3.9 | Python |
نحوه نصب
نصب پکیج whl fastqwiper-2021.1.58:
pip install fastqwiper-2021.1.58.whl
نصب پکیج tar.gz fastqwiper-2021.1.58:
pip install fastqwiper-2021.1.58.tar.gz