Package: macrel
Macrel: (Meta)genomic AMP Classification and RetrievalPipeline to mine antimicrobial peptides (AMPs) from (meta)genomes.If you use this software in a publication please citeSantos-Júnior CD, Pan S, Zhao X, Coelho LP. 2020.
Macrel: antimicrobial peptide screening in genomes and metagenomes.
PeerJ 8:e10555. DOI:10.7717/peerj.10555Run Macrel online:https://big-data-biology.org/software/macrelLicenseMIT.Macrel as a whole is under theMITlicense.InstallThe recommended method of installation is throughbioconda:condacreate--nameenv_macrel-cbiocondamacrel
condaactivateenv_macrel
macrel-hAlternatively, just:condainstall-cbiocondamacrelTo install from source,read the docsExamplesMacrel uses asubcommand interface. You runmacrel COMMAND ...with the
COMMAND specifying which components of the pipeline you want to use.To run these examples, first download the example sequences fromgithub, or
by running:macrelget-examplesThe main output file generated by Macrel consists of a table with 6 columns containing
the: sequence access code, peptide sequence, classification of peptide accordingly
composition and structure, the probability associated with the AMP prediction,
hemolytic activity prediction and probability associated to hemolytic activity
prediction. All peptides outputted in this table are considered AMPs (p > 0.5),
although peptides predicted as AMPs with probabilities closer to 1 are more likely
to be active.To run Macrel on peptides, use thepeptidessubcommand:macrelpeptides\--fastaexample_seqs/expep.faa.gz\--outputout_peptidesIn this case, we useexample_seqs/expep.faa.gzas the input sequence. This should
be an amino-acid FASTA file. The outputs will be written into a folder calledout_peptides, and Macrel will 4 threads. An example of output using
this mode can be found attest/peptides/expected.prediction.To run Macrel on contigs, use thecontigssubcommand:macrelcontigs\--fastaexample_seqs/excontigs.fna.gz\--outputout_contigsIn this example, we use the example fileexcontigs.fna.gzwhich is a FASTA
file with nucleotide sequences, writing the output toout_contigs.
An example of output using this mode can be found attest/contigs/expected.prediction.
Additionally to the prediction table, this mode also produces two files containing
general gene prediction information in the contigs and a fasta file containing the
predicted and filtered small genes (≤ 100 amino acids).To run Macrel on paired-end reads, use thereadssubcommand:macrelreads\-1example_seqs/R1.fq.gz\-2example_seqs/R2.fq.gz\--outputout_metag\--outtagexample_metagThe paired-end reads are given as paired files (here,example_seqs/R1.fq.gzandexample_seqs/R2.fq.gz). If you only have single-end reads, you can omit
the-2argument. An example of outputs using this mode can be found attest/reads/expected.predictionandtest/reads/expected.smorfs.faa.
Additionally to the prediction table, this mode also produces a contigs fasta file,
and the two files containing general gene prediction coordinates and a fasta file
containing the predicted and filtered small genes (≤ 100 amino acids).To run Macrel to get abundance profiles, you only need the short reads file
and a reference with peptide sequences. Use theabundancesubcommand:macrelabundance\-1example_seqs/R1.fq.gz\--fastaexample_seqs/ref.faa.gz\--outputout_abundance\--outtagexample_abundanceThis mode returns a table of abundances containing two columns, the first with the
name of the AMPs and the second with the number of reads mapped back to each peptide
using the given reference. An example of this output using the example file can be found
attest/abundances/expected.abundance.txt.CommunityMacrel is actively maintained to fix all issues and assimilate suggestions we
get from users (seeour commitments to high-quality
software).For general questions about macrel, we ask that you use theAMPSphere Google Group (mailing list).Technical issues can be reported usingGithub
issues.