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add: more details on cpp binary

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kuoi 2024-07-05 17:17:31 +10:00
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README.md
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@ -6,9 +6,9 @@ License: GPL-2.0-only
Author: Guoyi Zhang Author: Guoyi Zhang
# Requirements ## Requirements
## External software ### External software
- GNU Bash (provide cd) - GNU Bash (provide cd)
- GNU coreutils (provide cp mv mkdir mv) - GNU coreutils (provide cp mv mkdir mv)
@ -20,14 +20,14 @@ Author: Guoyi Zhang
- macse (default recognized path: /usr/share/java/macse.jar) - macse (default recognized path: /usr/share/java/macse.jar)
- GNU parallel - GNU parallel
## Internal software ### Internal software
- splitfasta (default recognized path: /usr/bin/splitfasta) - splitfasta (default recognized path: /usr/bin/splitfasta)
- sortdiamond (default recognized path: /usr/bin/sortdiamond) - sortdiamond (default recognized path: /usr/bin/sortdiamond)
# Arguments ## Arguments
## Details ### Details
``` ```
-c --contigs contings type: scaffolds or contigs -c --contigs contings type: scaffolds or contigs
@ -45,7 +45,7 @@ Author: Guoyi Zhang
for example: bash RGBEPP.sh -c scaffolds -f all -l list -g genes -r reference.aa.fasta for example: bash RGBEPP.sh -c scaffolds -f all -l list -g genes -r reference.aa.fasta
``` ```
## Directories Design ### Directories Design
``` ```
. .
@ -68,7 +68,7 @@ Each directory corresponds to each function.
`00_raw` should conatin all raw fastq.gz data. `00_raw` should conatin all raw fastq.gz data.
## Text Files ### Text Files
`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 `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
@ -86,9 +86,9 @@ grep '>' Reference.fasta | sed "s@>@@g" > genes
`reference.aa.fasta` can be replaced by another other name, but it must contain reference amino acids genome in fasta format `reference.aa.fasta` can be replaced by another other name, but it must contain reference amino acids genome in fasta format
# Progress ## Process
## RGBEPP.sh functions ### RGBEPP.sh functions
- Function clean: Quality control + trimming (fastp) - Function clean: Quality control + trimming (fastp)
- Function assembly: de novo assembly (spades) - Function assembly: de novo assembly (spades)
@ -99,9 +99,23 @@ grep '>' Reference.fasta | sed "s@>@@g" > genes
- Function merge: merge different taxa in the same reference exon gene to one fasta (RGBEPP.sh) - Function merge: merge different taxa in the same reference exon gene to one fasta (RGBEPP.sh)
- Function align: multiple sequence align based on Condon (macse) - Function align: multiple sequence align based on Condon (macse)
## Downstream process ### Downstream process
- concatenate sequences via SeqCombGo or catsequences or sequencematrix - concatenate sequences via SeqCombGo or catsequences or sequencematrix
- coalescent / concatenated phylogeny - coalescent / concatenated phylogeny
# sortdiamond
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)
Default sseq is column 2, qstart is column 8, etc.
Diamond default output format (--outfmt 6) does not contain qseq, you must custom the output format under output format 6.
# splitfasta
Usage: splitfasta sample.fasta
It always creates directories in the path that you run the splitfasta, and puts split fasta into the directory.