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Methods to determine sequence element (unitig) presence/absence
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README.md

unitig-caller

Determines presence/absence of sequence elements in bacterial sequence data. Currently uses assemblies as inputs (reads also possible by changing some options).

For small numbers of queries use --simple. For larger numbers (e.g. whole genome) use --index followed by --call.

Simple mode uses string matching after loading seqs into main memory. Index/call mode is a wrapper around squeakr and mantis.

Install

Use unitig_caller if installed through pip/conda, or python unitig_caller-runner.py if using a clone of the code.

With conda (recommended)

Get it from bioconda:

conda install unitig-caller

If you haven't set this up, first install miniconda. Then add the correct channels:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

With pip

Get it from PyPI:

pip install unitig_caller

Requires squeakr version 1.0 and mantis version 0.2.0 to run the --index and --call modes.

From source

Requires cmake, pthreads and a C++11 compiler (e.g. gcc >=4.8), in addition to the pip requirements.

git clone https://github.com/johnlees/unitig-caller
python setup.py install

Usage

Running simple mode

This uses code from seer to perform simple string matches:

unitig-caller --mode simple --strains strain_list.txt --unitigs queries.txt --output calls.txt

--strains is a file listing input assemblies, name followed by location of fasta file (tab separated), each on a new line. No header row.

--unitigs is a list of the unitig sequences to call. The unitigs need to be in the first column (tab separated). A header row is assumed, so output from pyseer etc can be directly used.

calls_unitigs.txt will contain unitig calls in seer/pyseer k-mer format.

Running with mantis

First create an index of all the sequences:

unitig_caller --index --strains strain_list.txt --output mantis_idx --cpus 8

Note this will require about 20Mb temporary disk space per strain, and the final step may be fairly RAM intensive. If this fails you can re-run without having to generate all the intermediate files again. Use of multiple CPUs is recommended, if available.

You can then use this index to rapidly call many unitig queries:

unitig_caller --call --unitigs queries.txt --output calls --mantis-index mantis_idx

Which will write to calls_unitigs.txt as in simple mode.

Option reference

usage: unitig-caller [-h] (--index | --call | --simple) [--strains STRAINS]
                     [--unitigs UNITIGS] [--output OUTPUT]
                     [--mantis-index MANTIS_INDEX] [--approximate]
                     [--kmer-size KMER_SIZE] [--count-cutoff COUNT_CUTOFF]
                     [--log-slots LOG_SLOTS] [--cpus CPUS] [--overwrite]
                     [--squeakr SQUEAKR] [--mantis MANTIS] [--version]

Call unitigs in a population dataset

optional arguments:
  -h, --help            show this help message and exit

Mode of operation:
  --index               Index sequences, before calling
  --call                Make calls from an indexed dataset
  --simple              Use string matching to make calls

Input/output:
  --strains STRAINS     List of strains to index
  --unitigs UNITIGS     List of unitigs to call
  --output OUTPUT       Prefix for output [default = 'mantis_index']
  --mantis-index MANTIS_INDEX
                        Directory containing mantis index (produced by index
                        mode) [default = 'mantis_index']

mantis/squeakr options:
  --approximate         Use approximate count mode [default = exact]
  --kmer-size KMER_SIZE
                        K-mer size for counts [default = 28]
  --count-cutoff COUNT_CUTOFF
                        Minimum k-mer count to be included [default = 1]
  --log-slots LOG_SLOTS
                        Starting log(number of count slots). Automatically
                        increased if necessary [default = 22]

Other:
  --cpus CPUS           Number of CPUs to use [default = 1]
  --overwrite           Overwrite existing output
  --squeakr SQUEAKR     Location of squeakr executable [default = squeakr]
  --mantis MANTIS       Location of mantis executable [default = mantis]
  --version             show program's version number and exit

Timing

Testing on 603 S. pneumoniae assemblies:

Test Mode Cores Time Memory Disk +tmp disk
Index Index 1 25.0min 12.7Gb 287Mb 10.7Gb
Index 4 13.3min 13.0Gb 287Mb 10.7Gb
100 unitigs Simple 1 27.4min 1.1Gb None None
Simple 4 9.3min 1.1Gb None None
Call 1 0.6s 34.1Mb Index Index
100k unitigs Call 1 2.9min 362Mb Index Index
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