This version of MerCat is depreciated please use the new updated version

https://github.com/raw-lab/mercat2

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MerCat: python code for versatile k-mer counter and diversity estimator for database independent property analysis (DIPA) obtained from metagenomic and/or metatranscriptomic sequencing data

Installing MerCat:

• Source:
  git clone https://github.com/raw-lab/mercat.git
  run python setup.py install
  

• Anaconda:
  Enable BioConda repo
  run conda install mercat
  

• PIP: We do not have a pip installer available as of now. If you would like to use pip, please install the modules listed in dependencies.txt via pip then others manually.

Usage:

• -i I path-to-input-file
• -f F path-to-folder-containing-input-files
• -k K kmer length
• -n N no of cores [default = all]
• -c C minimum kmer count [default = 10]
• -pro run mercat on protein input file specified as .faa
• -q tell mercat that input file provided are raw nucleotide reads as [.fq, .fastq]
• -p run prodigal on nucleotide assembled contigs. Must be one of ['.fa', '.fna', '.ffn', '.fasta']
• -t [T] Trimmomatic options
• -h, --help show this help message

By default mercat assumes that inputs provided is one of ['.fa', '.fna', '.ffn', '.fasta']

Example: To compute all 3-mers, run mercat -i test.fa -k 3 -n 8 -c 10 -p

The above command:

• Runs prodigal on test.fa, then runs mercat on the resulting protein file.
• Results are generally stored in input-file-name_{protein|nucleotide}.csv and input-file-name_{protein|nucleotide}_summary.csv
  • test_protein.csv and test_protein_summary.csv in this example
• test_protein.csv contains kmer frequency count, pI, Molecular Weight, and Hydrophobicity metrics for individual sequences.
• test_protein_summary.csv contains kmer frequency count, pI, Molecular Weight, and Hydrophobicity metrics for all unique kmers across all sequences in test.fa
• test_protein_diversity_metrics.txt containing the alpha diversity metrics.

Other usage examples:

• mercat -i test.fq -k 3 -n 8 -c 10 -q
  Runs mercat on raw nucleotide read (.fq or .fastq)

• mercat -i test.fq -k 3 -n 8 -c 10 -q -t
  Runs trimmomatic on raw nucleotide reads (.fq or .fastq), then runs mercat on the trimmed nucleotides

• mercat -i test.fq -k 3 -n 8 -c 10 -q -t 20
  Same as above but can provide the quality option to trimmomatic

• mercat -i test.fq -k 3 -n 8 -c 10 -q -t 20 -p Run trimmomatic on raw nucleotide reads, then run prodigal on the trimmed read to produce a protein file which is then processed by mercat

• mercat -i test.fna -k 3 -n 8 -c 10
  Run mercat on nucleotide input - one of ['.fa', '.fna', '.ffn', '.fasta']

• mercat -i test.fna -k 3 -n 8 -c 10 -p
  Run prodigal on nucleotide input, generate a .faa protein file and run mercat on it

• mercat -i test.faa -k 3 -n 8 -c 10 -pro
  Run mercat on a protein input (.faa)

• All the above examples can also be used with -f input-folder instead of -i input-file option

  • Example: mercat -f /path/to/input-folder -k 3 -n 8 -c 10 --- Runs mercat on all inputs in the folder

Citing Mercat

If you are publishing results obtained using MerCat, please cite:

White III RA, Panyala A, Glass K, Colby S, Glaesemann KR, Jansson C, Jansson JK. (2017) MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data. PeerJ Preprints 5:e2825v1 https://doi.org/10.7287/peerj.preprints.2825v1

CONTACT

Please send all queries to Ajay Panyala <ajay.panyala@gmail.com> and Richard Allen White III <richard.white@pnnl.gov> or <raw937@gmail.com>