105 lines
2.9 KiB
Markdown
105 lines
2.9 KiB
Markdown
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# RGB EPP
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Reference Genome based Exon Phylogeny Pipeline
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License: GPL-2.0-only
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Author: Guoyi Zhang
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# Requirements
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## External software
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- GNU Bash (provide cd)
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- GNU coreutils (provide cp mv mkdir mv)
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- GNU findutils (provide find)
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- fastp
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- spades.py (provided by spades)
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- diamond
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- java
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- macse (default recognized path: /usr/share/java/macse.jar)
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- GNU parallel
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## Internal software
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- splitfasta (default recognized path: /usr/bin/splitfasta)
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- sortdiamond (default recognized path: /usr/bin/sortdiamond)
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# Arguments
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## Details
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```
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-c --contigs contings type: scaffolds or contigs
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-g --genes gene file path
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-f --functions functions type (optional): all clean
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assembly fasta map pre split merge align
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-h --help show this information
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-l --list list file path
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-m --memory memory settings (optional, default 16 GB)
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-r --reference reference genome path
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-t --threads threads setting (optional, default 8 threads)
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--macse Macse jarfile path
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--sortdiamond sortdiamond file path
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--splitfasta splitfasta file path
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for example: bash RGBEPP.sh -c scaffolds -f all -l list -g genes -r reference.aa.fasta
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```
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## Directories Design
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```
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.
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├── 00_raw
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├── 01_fastp
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├── 02_spades
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├── 03_assemblied
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├── 04_diamond
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├── 05_pre
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├── 06_split
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├── 07_merge
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├── 08_macse
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├── genes
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├── list
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├── reference.aa.fasta
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└── RGBEPP.sh
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```
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Each directory corresponds to each function.
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## Text Files
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`list` is the text file containing all samples, if your raw data is following the style ${list_name}\_R1.fastq.gz and ${list_name}\_R2.fastq.gz, ${list_name} is what you should list in `list` file. The easy way to get it in Linux/Unix system is the following command
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```
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cd 00_raw
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ls | sed "s@_R[12].fastq.gz@@g" > ../list
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cd ..
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```
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`genes` is the text file containing all gene names from the reference fasta file. The easy way to get it in Linux/Unix system is the following command
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```
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grep '>' Reference.fasta | sed "s@>@@g" > genes
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```
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`reference.aa.fasta` can be replaced by another other name, but it must contain reference amino acids genome in fasta format
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# Progress
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## RGBEPP.sh functions
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- Function clean: Quality control + trimming (fastp)
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- Function assembly: de novo assembly (spades)
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- Function fasta: gather all fasta files from assembly directories (RGBEPP.sh)
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- Function map: local nucleic acids alignment search against amino acids subject sequence (diamond)
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- Function pre: generate corresponding sequences based on blast-styled output (sortdiamond)
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- Function split: splitting fasta sequence to directories based on the reference genome (splitfasta)
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- Function merge: merge different taxa in the same reference exon gene to one fasta (RGBEPP.sh)
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- Function align: multiple sequence align based on Condon (macse)
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## Downstream process
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- concatenate sequences via SeqCombGo or catsequences or sequencematrix
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- coalescent / concatenated phylogeny
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