https://github.com/sing-group/metatax
Metatax: Metataxonomics with a Compi-based pipeline for Precision Medicine
https://github.com/sing-group/metatax
Last synced: 6 months ago
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Metatax: Metataxonomics with a Compi-based pipeline for Precision Medicine
- Host: GitHub
- URL: https://github.com/sing-group/metatax
- Owner: sing-group
- License: other
- Created: 2021-03-16T10:35:17.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2021-03-17T08:46:33.000Z (over 5 years ago)
- Last Synced: 2026-01-15T05:04:20.509Z (6 months ago)
- Language: Dockerfile
- Size: 12.7 KB
- Stars: 0
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Metatax: Metataxonomics with a Compi-based pipeline for Precision Medicine.
Osvaldo Graña-Castro, Hugo López-Fernández, Alba Nogueira-Rodríguez, Florentino Fdez-Riverola, Fátima Al-Sharour and Daniel Glez-Peña.
A Docker image is available for this pipeline in [this Docker Hub repository](https://hub.docker.com/r/singgroup/metatax).
# Running the pipeline with sample data
It is possible to test the pipeline using our sample data available [here](). Download the ZIP file and decompress it in your local file system. Then, run the following command, changing the `/path/to/metataxonomics/data/` to the path where you have the decompressed data.
(i) Download sequencing data from SRA:
Read files can be downloaded from SRA (ID SRP116709) with the following command line (provided that Docker-CE is already installed):
*** Download first the required files SRR_Acc_List.txt, SraRunTable.txt, parameters.txt, map.tsv and uc_fast_params.txt from the following link: http://static.sing-group.org/software/compi/pipelines/metatax/supplementary-data-2019.08.08.zip
```
mkdir -p ./FASTQ
for SRR in $(cat SRR_Acc_List.txt) ; do echo $SRR; docker run -v ./FASTQ:/FASTQ --rm pegi3s/sratoolkit fastq-dump --origfmt --split-files --A $SRR -O ./FASTQ/ ; done
```
(ii) Data preprocessing:
As all the sequenced data in this dataset has been downloaded in step (i), we now select the samples we are working with (16S rRNA human sequences):
```
head -n 1 SraRunTable.txt > 16SrRNA_human.txt ; grep '^AMPLICON' SraRunTable.txt | grep 'Homo sapiens' >> 16SrRNA_human.txt
```
Then we collect the corresponding SRR* and patient codes for the selected samples to a separated file:
```
cut --output-delimiter=',' -f 15,20 16SrRNA_human.txt | grep -v 'Run' > listOfSelectedSamples.txt
```
In order to rename the samples in a clearer way, we rename them using the associated patient codes:
```
mkdir -p ./selectedFASTQ
for file in $(cat listOfSelectedSamples.txt); do echo $file; input=${file/,*/}; output=${file/*,/}; echo $input; echo $output; input1='./FASTQ/'${input}'_1.fastq'; input2='./FASTQ/'${input}'_2.fastq'; output1='./selectedFASTQ/'${output}'_1.fastq'; output2='./selectedFASTQ/'${output}'_2.fastq'; cp $input1 $output1; cp $input2 $output2; done
```
(iii) Executing metatax:
Copy parameters.txt, map.tsv and uc_fast_params.txt files to ./selectedFASTQ directory
Define a metatax execution variable:
```
metatax="docker run --rm -e DISPLAY="$(docker network inspect bridge --format='{{(index .IPAM.Config 0).Gateway}}'):0" -v ./selectedFASTQ:/data -v /tmp/COMPI_logs:/tmp -i compi/metatax"
```
Complete execution (all tasks):
```
$metatax --logs /tmp/ -pa /data/parameters.txt
```
Alternatively, single tasks can be excuted individually or even repeated as follows:
```
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task initialization
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task validate_mapping
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task join_pe
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task multiple_splitLibFastq
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task pick_otus
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task otu_table_summary
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task otu_table_single_rarefaction
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task otu_table_alpha_rarefaction
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task core_diversity
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task alpha_divers
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task beta_divers_through_plots
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task compare_alpha_divers
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task compare_categories
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task filter_otus
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task group_sig
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task align_sequences
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task phylogeny
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task univariate_DESeq2
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task univariate_edgeR
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task ancom
$metatax --logs /tmp/ -pa /data/parameters.txt --single-task selbal
```