Extras and Citation

Helpful command-line snippets

Contig length distribution of your input contigs

seqkit fx2tab -lg input.fasta \
  | awk -F "\t" '{print $4}' \
  | tail -n +2 \
  | hist -b 100 -s 10

Length distribution of contigs in ANI output (after filtering)

cat testing/gut_jaeger/nuc/gut_jaeger_virus_seqs_fasta_genome_ani.tsv \
  | awk -F "\t" '$8 > 0.1' \
  | awk -F "\t" '{print $3}' \
  | tail -n +2 \
  | hist -b 100 -x

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Citation

If you use skadi, please cite the underlying tools:

[MMSEQS2] MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.
          Steinegger M & Söding J. 2017. Nat. Biotech. 35, 1026–1028.
          https://doi.org/10.1038/nbt.3988

[PRODIGAL] Prodigal: prokaryotic gene recognition and translation initiation site identification.
           Hyatt et al. 2010. BMC Bioinformatics 11, 119.
           https://doi.org/10.1186/1471-2105-11-119.

[TAXONKIT] TaxonKit: A practical and efficient NCBI taxonomy toolkit.
           Shen, W. & Ren, H. J. 2021. Genet. Genomics.
           https://doi.org/10.1016/j.jgg.2021.03.006.