Getting started

Quick start

Install with mamba

mamba create -n mess mess

Run

mess test --bam

Output

📂mess_out
 ┣ 📂assembly_finder
 ┃ ┣ 📂download
 ┃ ┃ ┣ 📂GCF_000418345.1
 ┃ ┃ ┃ ┗ 📜GCF_000418345.1_ASM41834v1_genomic.fna.gz
 ┃ ┃ ┣ 📂GCF_003812505.1
 ┃ ┃ ┃ ┗ 📜GCF_003812505.1_ASM381250v1_genomic.fna.gz
 ┃ ┃ ┗ 📜.snakemake_timestamp
 ┃ ┣ 📜archive.zip
 ┃ ┣ 📜assembly_finder.log
 ┃ ┣ 📜assembly_summary.tsv
 ┃ ┣ 📜config.yaml
 ┃ ┣ 📜sequence_report.tsv
 ┃ ┗ 📜taxonomy.tsv
 ┣ 📂bam
 ┃ ┣ 📜sample1.bam
 ┃ ┣ 📜sample1.bam.bai
 ┃ ┣ 📜sample2.bam
 ┃ ┗ 📜sample2.bam.bai
 ┣ 📂fastq
 ┃ ┣ 📜sample1_R1.fq.gz
 ┃ ┣ 📜sample1_R2.fq.gz
 ┃ ┣ 📜sample2_R1.fq.gz
 ┃ ┗ 📜sample2_R2.fq.gz
 ┣ 📂processing
 ┃ ┣ 📜cov.tsv
 ┃ ┗ 📜split.tsv
 ┣ 📂tax
 ┃ ┣ 📜sample1_profile.txt
 ┃ ┗ 📜sample2_profile.txt
 ┣ 📜config.yaml
 ┗ 📜mess.log

Step-by-step guide