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https://github.com/abhijeetsingh1704/acetoscan

AcetoScan - Automated pipeline for the unsupervised analysis of FTHFS amplicon sequencing
https://github.com/abhijeetsingh1704/acetoscan

acetobase acetogens amplicon-sequencing analysis-pipeline fthfs

Last synced: 25 days ago
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AcetoScan - Automated pipeline for the unsupervised analysis of FTHFS amplicon sequencing

Host: GitHub
URL: https://github.com/abhijeetsingh1704/acetoscan
Owner: abhijeetsingh1704
License: other
Created: 2019-05-07T09:07:26.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2021-08-27T08:04:44.000Z (over 3 years ago)
Last Synced: 2024-04-16T18:35:10.402Z (8 months ago)
Topics: acetobase, acetogens, amplicon-sequencing, analysis-pipeline, fthfs
Language: Shell
Homepage:
Size: 46.1 MB
Stars: 4
Watchers: 4
Forks: 3
Open Issues: 2
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

# AcetoScan

- Version: 1.0
- Last modified: Thu Sep 3 12:52:30 CEST 2020
- Sign: Abhijeet Singh ([email protected])

## Description

AcetoScan is a software pipeline for the analysis of Illumina MiSeq sequencing data for the FTHFS (Formyl--tetrahydrofolate synthetase) gene/amplicons

AcetoScan can also process fasta sequences to filter out non-target sequences, assigning taxonomy to the FTHFS fasta sequences and generate phylogenetic tree (see AcetoScan commands)

## Dependencies

`AcetoScan` pipeline uses some software dependencies (version equals or higher)
```
- Cutadapt (2.9)
- VSEARCH (2.13.1)
- NCBI-blast+ (2.5.0+)
- Bioperl (1.7.2-3)
- MAFFT (7.307)
- Fasttree (2.1.9)
- R (3.5.2), with libraries:
¤ phyloseq (1.24.2)
¤ ggplot2 (3.1.1)
¤ plotly (4.9.0)
¤ RColorBrewer (1.1.2)
¤ plyr (1.8.4)
¤ dplyr (0.8.0.1)
¤ vegan (2.5.6)
```

## Installation

For installation run the following command in terminal, this will check all dependencies and download the reference database from acetobase website.

```
$ chmod +x install_linux.sh OR install_mac.sh

$ sudo ./install_linux.sh OR install_mac.sh
```

## Installation without sudo/ROOT

For installation as local user make sure the dependency software are installed and modules are loaded (on server environment)
```
bash install_linux.sh OR install_mac.sh
```

## acetoscan installation

`install_linux.sh` OR `install_mac.sh` will create main directory `acetoscan` in `$HOME` and sub-directories

```
1. bin - containing all main AcetoScan command scripts
2. dat - containing test
3. db - containing reference database AcetoBase
4. doc - containing user manual and tutorial video
5. scripts - containing dependencies scripts
```

## AcetoScan input
```
1. user_data_directory - containing input raw data
```
###### Raw data must in format "Samplename_XYZ_L001_R1_001.fastq.(gz or bz2)"
https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/miseqreporter/miseq-reporter-generate-fastq-workflow-guide-15042322-01.pdf, page 9, FASTQ File Names

## AcetoScan output

`acetoscan` will result in two directories

- Directories will be created `in default/destination path`

```
1. output_data - containing process data will be generated and stored. In case of process failure, data can be accessed from here for further processing

2. acetoscan_result - containing all the final graphics, OTU table and TAX table. After successful execution of analysis, all the important data will be copies to this final directory.
```

## AcetoScan commands

```
$ acetoscan -X

$ /$HOME/acetoscan/acetoscan -X
```

```

1. acetoscan - for complete processing of raw sequence data
2. acetocheck - for processing fasta sequences and filter out non-target sequences
3. acetotax - acetocheck + taxonomic assignments
4. acetotree - acetotax + phylogenetic tree generation
```

## Using acetoscan program

Use `acetoscan` as follows

```
acetoscan -i // [-o //] [-m 300] [-n 120] [-q 20] [-l 24] [-r 1] [-t 0.80] [-c 2] [-e 1e-3] [-B 1000] [-P 8]

-i Input directory containing raw illumina data
-o Output directory
:default = /$HOME/acetoscan/output_data
-m Maximum length of sequence after quality filtering
:default max_length = 300
-n Minimum length of sequence after quality filtering
:default min_length = 120
-q Quality threshold for the sequences
:default quality threshold = 20
-l Primer length
:default primer length = 24
-r Read type either forward or reverse reads
1 = forward reads (default), 2 = reverse reads
-t Clustering threshold
:default cluster threshold = 0.80 (80 %)
-c Minimum cluster size
:default minimum cluster size = 2
-e E-value
:default evalue = 1e-3
-B Bootstrap value
:default bootstrap = 1000
-P Parallel processes / threads
:default no. of parallels = all available threads
-h Print help
-X Print AcetoScan commands
-v Print AcetoScan version
-C Print AcetoScan citation

```

## acetocheck
Use this command for the FTHFS fasta a sequences and filter out any unspecific / non-FTHFS sequence

```
$ acetocheck -h

```

```
acetocheck -i /path/ [-o /path/] [-e 1e-3] [-P 8]

-i Input file - multifasta file
-o Output file
:default = acetocheck__.fasta
-e E-value
:default evalue = 1e-3
-P Parallel processes/threads
:default no. of parallels = all available threads
-h Print help
-X Print AcetoScan commands
-v Print AcetoScan version
-C Print AcetoScan citation
```

### Use
```
acetocheck -i /home/abhi/Desktop/seq.fasta -o /home/abhi/Desktop/my_sequences -e 1e-3 -P 8
```
#### output
1. my_sequences.fasta
2. acetotax_< Date >_< Time >.log

## acetotax
Use this command for the FTHFS fasta a sequences and filter out any unspecific / non-FTHFS sequence and taxonomic annotations of the fasta sequences

```
$ acetotax -h

```

```
acetotax -i /path// [-o /path//] [-e 1e-3] [-P 8]

-i Input_file
-o Output file
:default = acetotax__.csv
:default = acetotax__.fasta
-e E-value
:default evalue = 1e-3
-P Parallel processes/threads
:default no. of parallels = all available threads
-h Print help
-X Print AcetoScan commands
-v Print AcetoScan version
-C Print AcetoScan citation
```

### Use
```
acetotax -i /home/abhi/Desktop/seq.fasta -o /home/abhi/Desktop/my_sequences -e 1e-3 -P 8
```
#### output
1. my_sequences.fasta
2. my_sequences.csv
3. acetotax_< Date >_< Time >.log

## acetotree
Use this command for the FTHFS fasta a sequences and filter out any unspecific / non-FTHFS sequence and taxonomic annotations of the fasta sequences and generation of phylogenetic tree

```
$ acetotree -h

```

```
acetotree -i /path/ [-o /path/] [-e 1e-3] [-B 1000] [-P 8]

-i Input file - multifasta file
-o Output file
:default = acetotree__.fasta
:default = acetotree__.csv
:default = acetotree__.aln
:default = acetotree__.tree
-e E-value
:default evalue = 1e-3
-B Bootstrap value
:default bootstrap = 1000
-P Parallel processes/threads
:default no. of parallels = all available threads
-h Print help
-X Print AcetoScan commands
-v Print AcetoScan version
-C Print AcetoScan citation
```

### Use
```
acetotree -i /home/abhi/Desktop/seq.fasta -o /home/abhi/Desktop/my_sequences -e 1e-3 -B 1000 -P 8
```
#### output
1. my_sequences.fasta
2. my_sequences.csv
3. my_sequences.aln
4. my_sequences.tree
5. acetotax_< Date >_< Time >.log

# Running AcetoScan Pipelline as a Docker image/container

### Mounting the local volume / connecting the files on local computer to the container

`
sudo docker volume create --opt type=none --opt o=bind --opt device=/PATH/to/my/DATA --name MY_CUSTOM_NAME
`
#### Example
###### Here
`--opt device=` - will have the path to your raw input data

`--name` - any name according to your wish

`
sudo docker volume create --opt type=none --opt o=bind --opt device=/home/abhi/Desktop/reads --name myDockerAcetoscan
`

### Running docker image as container
##### NOTE: only `MY_CUSTOM_NAME` should be changed according to your `--name` flag

`
sudo docker run --rm -v MY_CUSTOM_NAME:/acetoscan/input_dir -it abhijeetsingh1704/acetoscan -i /acetoscan/input_dir
`
#### Example
`
sudo docker run --rm -v myDockerAcetoscan:/acetoscan/input_dir -it abhijeetsingh1704/acetoscan -i /acetoscan/input_dir
`
###### Default program for AcetoScan pipeline is `acetoscan` command, therefore it is optional to call it with `--entrypoint` flag. But in case of `acetocheck`,`acetotax` or `acetotree` command the code need to include `--entrypoint` flag

#### Example
##### acetoscan
`
sudo docker run --rm -v myDockerAcetoscan:/acetoscan/input_dir --entrypoint acetoscan -it abhijeetsingh1704/acetoscan -i /acetoscan/input_dir
`
##### acetocheck

`
sudo docker run --rm -v myDockerAcetoscan:/acetoscan/input_dir --entrypoint acetocheck -it abhijeetsingh1704/acetoscan -i /acetoscan/input_dir/input_file.fasta
`

- OR

`
sudo docker run --rm -v myDockerAcetoscan:/acetoscan/input_dir --entrypoint acetocheck -it abhijeetsingh1704/acetoscan -i /acetoscan/input_dir/input_file.fasta -o /acetoscan/input_dir/output_file.fasta
`

# Citation

Singh A, Nylander JAA, Schnürer A, Bongcam-Rudloff E and Müller B (2020) High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure. Front. Microbiol. 11:2066. doi: 10.3389/fmicb.2020.02066