thh32 / spherical

Spherical is an iterative approach to large metagenome assemblies, designed for clusters where insufficient RAM is available for a straightforward assembly.

Spherical

Spherical is an iterative approach to assembling metagenomic datasets. Spherical has been designed to produce a more complete assembly from deep sequenced metagenomic data. Utilization of multiple iterations of assembly allows for regions which otherwise would be missed to be assembled without a reduction in contig accuracy. Another use for Spherical is its ability to produce metagenomic assemblies using a subset of the initial input file, allowing for assembly of a metagenome whilst using a fraction of the RAM that would otherwise be required.

Requirements

• Python 2.7
• Velvet (tested using version 1.2.10)
• Bowtie2 (tested using version 2.2.3)

Python modules;

• Numpy
• HTSeq

Usage

Once all dependancies are install and Spherical has been downloaded you can begin using Spherical from command line.

The most basic use of Spherical is;

python Spherical.py -fasta -i $INPUT -velvet -bowtie2 -o $OUTPUT

Tutorial

To ensure all the dependancies for Spherical are correctly installed and get you used to the various options of Spherical there is a test dataset.

The test dataset consists of a Chicken cecum microbiome dataset obtained from MG-RAST (entry;101).

python Spherical.py -fasta -m -k 21 -R 1 -align 99 -iter 5 -i test_data.fa -velvet -bowtie2 -o test_assembly

In this command we tell Spherical to produce an assembly using Velvet as the assembler and Bowtie2 as the aligner. The subsample size given of the input data to Velvet is 1 which means the entire file is to be used. Velvet will use a kmer size of 21 and only finish once either the alignment rate reaches 99% or Spherical has completed 5 iterations of assembly. Finally we have also used the -m command to tell Spherical to combine the finished assemblies into a single file.

This will produce an output assembly titled test_assembly.combined.fa which when compared using the code below the value 0 should be returned.

grep -F -x -v -f test_assembly.combined.fa provided_assembly.fa |grep '>'| wc -l

A value other than 0 inicates that an error has occured during the assembly process leading to a difference between the assemblies. This is most likely due to the user using a different version of Velvet or Bowtie2.

Options

Full customisation of Spherical is possible using the commands below.

Option command	Description	Default
-align $INT	Identifies an alignment rate that must be obtained before Spherical stops producing iterations	70
-iter $INT	States the number of iterations that must be produced	5
-k $INT	Sets the Kmer size which should be used for each assembly	31
-R $FLOAT	States the input size which should be used in each iteration of assembly e.g. -R 0.25 = 25% of reads	NA
-limit	A switch which prevents contigs smaller from 300bp from being produced	NA
-m	A switch which activates the combination of all iterations assemblies at the end to produce a final file	NA
-fasta	States that the input file is in FASTA input	NA
-fastq	States that the input file is in FASTQ input	NA
-i $FILE	Identifies the input file	NA
-o $FILE	Identifies string to be used for output file	NA
-bowtie2	Identifies Bowtie2 as the aligner of choice	NA
-velvet	Identifies Velvet as the assembler of choice	NA
-x1 $STRING	Allows additional options for assembly to be used in Velveth or ABYSS steps, used for options starting with '-'	NA
-x2 $STRING	Allows additional options for assembly to be used in Velveth or ABYSS steps, used for options starting with '--'	NA

spherical's Issues

Bowtie2-align error

Hello,
When running the tutorial as described in README, I get the following bowtie2-align error (see this gist for full output and command line used).

Error: Must specify at least one read input with -U/-1/-2
(ERR): bowtie2-align exited with value 1

Overall, Spherical seemed to work OK since I got 225,474 contigs in test_assembly.combined.fa. It is different from provided_assembly.fa which contains 226,578 contigs.

Thank you...Paul

Spherical.py: error: argument -x: expected one argument

Hi...I'm trying the tutorial assembly with the abyss assembler. Since abyss trims lowercase characters by default, I need to use the --no-trim-masked option. However, when I add that option using -x --no-trim-masked, I get an error:

~/local/opt/miniconda2/bin/python Spherical.py -fasta -m -k 21 -R 1 -align 99 -iter 5 -i test_data.fa -abyss -bowtie2 -o test_assembly -x --no-trim-masked
usage: Spherical.py [-h] [-i INPUT] [-o OUTPUT] [-fasta] [-fastq] [-limit]
                   [-velvet] [-abyss] [-megahit] [-bwa] [-bowtie2]
                   [-align ALIGNMENTRATE] [-iter ITERATIONS] [-m] [-k KMER]
                   [-R RAM] [-x EXTRA] [-u BOWTIE_EXTRA] [-f]
Spherical.py: error: argument -x: expected one argument

Thank you