a 16S pipeline
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merge.py
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van.py

README.md

caravan

Caravan is a fork of SmileTrain that I made in order to

  • rework the command-line interface
  • change in the intermediate file types (into yaml)
  • change the submission style (to explictly use ssub)
  • move simple functions to quick perl tools

Caveat: This readme has fallen a little behind, especially when it comes to the initial data format and the possibilities for merging.

caravan requirements

  • caravan is developed against Python 3.4 and Perl 5.10.1.
  • Biopython

Getting started

First, you'll need to have your data in a standard input format:

  • All fastq files must be in Illumina 1.8+ format (also known as Sanger, Phred+33, or ASCII offset 33). You can convert fastq files in older Illumina format (i.e., Phred+64) using van.py convert.
  • Intersecting multiple files requires that they have IDs like readXXX, where XXX are monotonically increasing integers. You can get your fastq files into this format using van.py convert --rename.
  • When dereplicating, if you want provenience data (i.e., to make an OTU table), then the reads must have IDs with a sample=XXX field. A field is separate from other parts of the ID my semicolons. The preferred read ID format is like read1234;sample=sample1.

Suggested workflow for paired-end reads

Newer versions of caravan use the new three file Illumina format: forward reads in one fastq, reverse reads in a second, and the index reads (aka "barcode reads") in a third.

  1. Trim primers from the forward and reverse fastq's (using van.py primer).
  2. Demultiplex the index reads (using van.py demultiplex).
  3. Intersect the forward, reverse, and mapping information (using van.py intersect).
  4. Merge the forward and reverse reads (using van.py merge).
  5. Quality filter the merged reads (using van.py filter).
  6. Dereplicate and provenance (using van.py derep).
  7. Make OTUs.

If you do not have paired-end reads, you'll probably want to use van.py truncate to trim sequences by their quality or length.

Note that, if using van.py rdp on a reverse read, you will want to use the --antisense option. Caravan throws out RDP classifications made using reverse complements because, if we don't expect a reverse complement, it's probably a bad classification.

Documentation

There is sparse documentation. Sorry. But the --help option is usually pretty explanatory.

Tests

Unit tests are in the test folder. You can run the tests from the top directory by running py.test or make.

Unit tests are mostly incomplete. Sorry. I'm a terrible programmer.