Lab Stuff

This repository contains general scripts to automatize the routine tasks of my work at WallauLab. For some scripts, I added test files in the directory /test_files

Usage

To format LTR_finder output:

python LTR\_finder\_to\_csv.py -in

To assembly mitogenomes using a reference-guided approach with MITObin:

bash mito.sh <reference_genome> <adapter_path/adapter_file> <trimmomatic_path/trimmomatic_jar> </home/user/mira_path/> <num_threads>
#example line:
bash mito.sh ref_genome1.fasta sracode_1.fastq sracode_2.fastq Trimmomatic-0.36/adapters/adapter_file.fa ~/softwares/Trimmomatic-0.36/trimmomatic-0.36.jar /home/user/softwares/mira_4.0.2/ 8

To automatize auto_mito.sh

bash auto_mito.sh <genomes_fastq_adapters.lst> <path/trimmomatic> <path/mira> <num_threads>
#example line
bash auto_mito.sh genomes_fastq_adapters.lst ~/softwares/Trimmomatic-0.36/trimmomatic-0.36.jar /home/user/softwares/mira_4.0.2/ 8

To download fastq files from a file with a number or SRA codes

bash sra.sh <sra_file_list.txt>

To execute cd-hit getting a tsv formatted file of clusters

python cd_hit_formated.py -in <fasta_file> -p -m -cd "cd-hit line" -md
#example line for nucleotides:
python cd_hit_formated.py -in sequences.fasta -p 16 -m 60000 -cd "-c 0.8 -aL 0.8 -g 1 -d 200"
#example line for proteins:
python cd_hit_formated.py -in sequences.fasta -p 16 -m 60000 -cd "-c 0.8 -aL 0.8 -g 1 -d 200" -md prot

To execute DNAsp2tsv.py

python DNAsp2tsv.py -in DNAsp_output.txt

To execute nwk2nexus.py

python nwk2nexus.py -in tree.nwk -o tree.nexus

Disclaimer

• This repository will be constantly updated.