MetaFinisherSC

Introduction

To run the tool, you should have input files(contigs.fasta, raw_reads.fasta) in destinedFolder. The tool will first run through FinisherSC to generate improved2.fasta to destinedFolder. Then it will go through the newly added functions suitable for metagenomics study and the final output file is abun.fasta The command to run MetaFinisherSC to use 20 threads(-par 20) is thus as follows.

    python finisherSCCoreLib/finisherSC.py -par 20 destinedFolder/ mummerPath/

    python aSplitter.py -par 20 -rp improved2.fasta -ar True -rs 0 -rd True destinedFolder/ mummerPath/

A test set is located here https://www.dropbox.com/sh/slahcgv55037aiv/AAAzkaP6HILdBlH2G_xapKYHa?dl=0

If you have enough computing resources, you can run

    python finisherSCCoreLib/finisherSC.py -par 48 destinedFolder/ mummerPath/

    python aSplitter.py -par 48 -rp improved2.fasta destinedFolder/ mummerPath/

Example

Below is a step by step example on running MetaFinisherSC on the testset provided.

1. Clone MetaFinisherSC

    git clone https://github.com/kakitone/MetaFinisherSC.git
   

2. Get into the MetaFinisherSC folder, create directory to hold the data, download data from Dropbox and check to see if you get everything(contigs.fasta, raw_reads.fasta, reference.fasta).

    cd MetaFinisherSC/        
   
    mkdir dataFolder
    
    cd dataFolder
    
    wget -O testset.zip  https://www.dropbox.com/sh/slahcgv55037aiv/AAAzkaP6HILdBlH2G_xapKYHa?dl=1
    
    unzip testset.zip
    
    ls -lt
   

3. Go back to the main directory containing MetaFinisherSC and run the following two commands. Here we assume that /usr/bin/ is the path to your MUMmer. This step can take a few minutes.

    cd ../
   
    python finisherSCCoreLib/finisherSC.py -par 20 dataFolder/ /usr/bin/
    
    python aSplitter.py -par 20 -rp improved2.fasta -ar True -rs 0 -rd True dataFolder/ /usr/bin/
   

4. Now verify that the original contigs.fasta contain 4 contigs whereas the final abun.fasta contains 2 contigs

    fgrep -o ">" dataFolder/contigs.fasta  | wc -l
    
    fgrep -o ">" dataFolder/abun.fasta  | wc -l
   

5. Align the abun.fasta with reference.fasta.

    nucmer dataFolder/abun.fasta dataFolder/reference.fasta         
   
    show-coords out.delta
   

6. You should now see

NUCMER

[S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] | [TAGS]

1 5000000 | 5000000 1 | 5000000 5000000 | 100.00 | Segkk0 Segkk0

1 5000000 | 5000000 1 | 5000000 5000000 | 100.00 | Segkk1 Segkk1