155 lines
4.6 KiB
Markdown
155 lines
4.6 KiB
Markdown
# 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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- fastp
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- spades.py (provided by spades)
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- diamond
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- bowtie2
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- samtools
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- bcftools
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- exonerate (optional, only for --codon)
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- java
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- macse (default recognized path: /usr/share/java/macse.jar)
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- trimal
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### Internal software
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- sortdiamond (default recognized path: /usr/bin/sortdiamond)
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- delstop (default recognized path: /usr/bin/delstop)
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## Arguments
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### Details
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```
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-c --config config file for software path (optional)
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-g --genes gene file path (optional, if -r is specified)
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-f --functions functions type (optional): all clean assembly
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map postmap varcall consen codon align trim
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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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--codon Only use the codon region (optional)
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--fastp Fastp path (optional)
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--spades Spades python path (optional)
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--diamond Diamond python path (optional)
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--sortdiamond SortDiamond python path (optional)
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--bowtie2 Bowtie2 path (optional)
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--samtools Samtools path (optional)
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--bcftools Bcftools path (optional)
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--exonerate Exonerate path (optional)
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--macse Macse jarfile path (optional)
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--delstop Delstop path (optional)
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--trimal Trimal path (optional)
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for example: ./RGBEPP -f all -l list -t 8 -r reference.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_bowtie2
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├── 04_bam
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├── 05_vcf
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├── 06_consen
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├── 07_macse
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├── 08_trimal
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├── list
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├── gene
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├── reference.aa.fasta
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└── RGBEPP
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```
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Each directory corresponds to each function.
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`00_raw` should conatin all raw fastq.gz data.
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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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## Process
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### RGBEPP 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 map: local nucleic acids alignment search against amino acids subject sequence (diamond, sortdiamond), mapping raw reads to its scaffolds sequences (bowtie2)
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- Function postmap: Sorting and marking the read read alignment (samtools)
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- Function varcall: variant calling and filtering (bcftools)
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- Function consen: get consensus fasta file from vcf files (bcftools), then sort sequences based on gene name and taxa name (RGBEPP)
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- Function codon (optional): only extract the exon sequence (exonerate)
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- Function align: multiple sequence align based on condon (macse)
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- Function trim: trimming based on codon (trimal, delstop)
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### Arguments reuqirements for functions
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| Functions | -g/--gene | -l/--list | -r/--reference |
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| --------- | --------- | --------- | -------------- |
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| clean | | ✔ | |
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| assembly | | ✔ | |
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| map | | ✔ | ✔ |
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| postmap | | ✔ | |
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| varcall | | ✔ | |
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| consen | ✔ | ✔ | |
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| codon | ✔ | | ✔ |
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| align | ✔ | | |
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| trim | ✔ | | |
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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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## Inner software
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### sortdiamond
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Usage: `sortdiamond diamond_output.m8 generated.fasta sseq,qstart,qend,bitscore/evalue,qseq(optional, default 1,6,7,11,17, start from 0) bitscore/evalue(optional, default bitscore)`
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Default sseq is column 2, qstart is column 8, etc.
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Diamond default output format (--outfmt 6) does not contain qseq, you must custom the output format under output format 6.
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### delstop
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`delstop <fasta_aa> <fasta_nt> --delete`
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Delete StopCondon generated by Macse. fasta_aa and fasta_nt should be macse output files, `--delete` should be used when downstream software is tirmal
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### splitfasta
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Usage: `splitfasta sample.fasta`
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It always creates directories in the path that you run the splitfasta, and puts split fasta into the directory.
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