REAGO 1.1 has been released at https://github.com/chengyuan/reago-1.1
an assembly tool for 16S ribosomal RNA recovery from metagenomic data
Dependencies:
- Infernal 1.1.1
- Readjoiner 1.2
Runbook:
Input: Paired-end metagenomic reads in FASTA format
Output: 16S genes recovered from metagenomic reads
Step 1: Identify 16S reads.
command: 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 0.8
-e ERROR_CORRECTION_THRESHOLD, default 0.05
-t TIP_SIZE, default 30
-b PATH_FINDING_PARAMETER, default 10
example: python reago.py make_sample/sample/filetered.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.