Microbiology Encyclopedia

Genomics Command-Line Cheatsheet

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Genomics Command-Line Cheatsheet

Study aid

Commands are illustrative templates for learning the shape of a workflow, not validated clinical procedures. Always check current tool documentation and versions (Reproducible Bioinformatics Workflows).

1. Inspect and QC reads

fastqc sample_R1.fastq.gz sample_R2.fastq.gz -o qc/
multiqc qc/ -o qc/
 
fastp -i sample_R1.fastq.gz -I sample_R2.fastq.gz \
      -o clean_R1.fastq.gz -O clean_R2.fastq.gz \
      --detect_adapter_for_pe --html fastp.html

Coverage sanity check: coverage ≈ (num_reads × read_len) / genome_size

2. Contamination screen

kraken2 --db k2_standard --paired clean_R1.fastq.gz clean_R2.fastq.gz \
        --report kraken.report --output /dev/null

3. Assemble

# short reads
shovill --R1 clean_R1.fastq.gz --R2 clean_R2.fastq.gz --outdir asm --cpus 8
 
# long reads
flye --nano-hq ont.fastq.gz --out-dir asm_ont --threads 8
 
quast.py asm/contigs.fa -o asm_qc

4. Annotate

bakta --db bakta_db --output ann --prefix sample asm/contigs.fa
# or
prokka --outdir ann --prefix sample asm/contigs.fa

5. Typing

mlst asm/contigs.fa
kleborate -a asm/contigs.fa -o kleborate.txt --all   # Klebsiella

6. AMR and plasmids

amrfinder -n asm/contigs.fa -O Escherichia --plus -o amr.tsv
abricate --db plasmidfinder asm/contigs.fa
mob_recon --infile asm/contigs.fa --outdir mob_out

7. Mapping and variants

bwa-mem2 index ref.fa
bwa-mem2 mem -t 8 ref.fa clean_R1.fastq.gz clean_R2.fastq.gz \
  | samtools sort -o sample.bam
samtools index sample.bam
 
bcftools mpileup -f ref.fa sample.bam | bcftools call -mv --ploidy 1 -Oz -o sample.vcf.gz
bcftools index sample.vcf.gz
 
# or the wrapper most microbial labs use
snippy --outdir snp_out --ref ref.gbk --R1 clean_R1.fastq.gz --R2 clean_R2.fastq.gz
snippy-core --ref ref.gbk snp_out_*/

8. Phylogeny

run_gubbins.py core.full.aln --prefix gubbins      # mask recombination
iqtree2 -s core.aln -m GTR+G -B 1000 -T AUTO       # ML tree + ultrafast bootstrap

9. Pangenome

panaroo -i ann/*.gff3 -o pangenome --clean-mode strict -t 8

10. Metagenomics

metaphlan reads.fastq.gz --input_type fastq -o profile.txt
metaspades.py -1 R1.fq.gz -2 R2.fq.gz -o meta_asm
metabat2 -i meta_asm/contigs.fasta -a depth.txt -o bins/bin
checkm lineage_wf bins/ checkm_out -x fa

11. Reproducible run

nextflow run nf-core/bactmap -profile docker \
  --input samplesheet.csv --reference ref.fa --outdir results

Graph View

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