REAGO v1.1

Changes:

• Refactored the entire workflow, making code easier to follow.
• Fixed various bugs.

To cite REAGO

MLA

Yuan, Cheng, et al. "Reconstructing 16S rRNA genes in metagenomic data." Bioinformatics 31.12 (2015): i35-i43.

Tex

@article{yuan2015reconstructing,
  title={Reconstructing 16S rRNA genes in metagenomic data},
  author={Yuan, Cheng and Lei, Jikai and Cole, James and Sun, Yanni},
  journal={Bioinformatics},
  volume={31},
  number={12},
  pages={i35--i43},
  year={2015},
  publisher={Oxford Univ Press}
}

Manual

an assembly tool for 16S ribosomal RNA recovery from metagenomic data

Dependencies:

• Infernal 1.1.1
• Readjoiner 1.2 (http://genometools.org/pub/nightly_builds/)

Runbook:

Input: Paired-end metagenomic reads in FASTA format

Output: 16S genes recovered from metagenomic reads

Step 1: Identify 16S reads.

python filter_input.py paired_end_1.fasta paired_end_2.fasta output_dir cm_dir cm_to_use num_of_CPU

Example:

python filter_input.py sample_1.fasta sample_2.fasta filter_out cm ba 10

Step 2: Assemble 16S reads.

command: python reago.py filename.fasta -l READ_LENGTH

Optional parameters:

• -o OVERLAP, default 0.7
• -e ERROR_CORRECTION_THRESHOLD, default 0.05
• -t TIP_SIZE, default 30
• -b PATH_FINDING_PARAMETER, default 10

Example:

python reago.py filter_out/filtered.fasta sample_out -l 101

Note:

REAGO assumes the sequence names of a read pair to be XXXX.1 & XXXX.2. The only difference of their names is the last character.