Verdanta provides quality control plots and precomputed gene expression tables. These data are computed using the following pipeline.

  • prefetch (v3.2.1)

    • Command: 
      prefetch {sra_id} --max-size {MAX_SIZE_GB}g

  • fasterq-dump (v3.2.1)

    • Command: 
      fasterq-dump --threads {THREADS} --split-files {sra_id}

  • fastp (v0.24.0)

    • Paired-end reads: 
      fastp \
  --thread {THREADS} \
  -i "{rd}/{sra}_1.fastq" \
  -I "{rd}/{sra}_2.fastq" \
  -o "{sra}_1.trimmed.fastq" \
  -O "{sra}_2.trimmed.fastq"
    • Single-end reads: 
      fastp \
  --thread {THREADS} \
  -i "{rd}/{sra}.fastq" \
  -o "{sra}.trimmed.fastq"

  • salmon (v1.10.1)

    • Index generation: 
      salmon index \
  -t {transcriptome} \
  -i {index} \
  -k 31 \
  --keepDuplicates
    • Quantification (paired-end): 
      salmon quant \
  -i {idx} \
  -l A \
  -1 {fd}/{sra}_1.trimmed.fastq \
  -2 {fd}/{sra}_2.trimmed.fastq \
  -o {out} \
  --writeMappings {out}/mappings.sam \
  -p {CPU_COUNT} \
  --geneMap {gm}
    • Quantification (single-end): 
      salmon quant \
  -i {idx} \
  -l A \
  -r {fd}/{sra}.trimmed.fastq \
  -o {out} \
  --writeMappings {out}/mappings.sam \
  -p {CPU_COUNT} \
  --geneMap {gm}

  • thaf (v0.0.2) (developed by Verdanta, open source)

    • Command: 
      thaf \
  -f {gff3} \
  -g {gene_map} \
  -d {genomic_fasta} \
  -t {transcriptome} \
  {features}

  • fastqc (v0.11.9)

    • Paired-end reads: 
      fastqc \
  "{rd}/{sra}_1.fastq" \
  "{rd}/{sra}_2.fastq" \
  --outdir "{wd}" \
  --threads {THREADS} \
  --quiet
    • Single-end reads: 
      fastqc \
  "{rd}/{sra}.fastq" \
  --outdir "{wd}" \
  --threads {THREADS} \
  --quiet
  • rust-htslib (v0.50)
  • bio (v2.3)

Please contact us if you have any questions about the pipeline, or want to propose changes or extensions.