/MAEP-Python

MAEP(Metagenomics Assebly Evaluation Pipeline).This pipeline is a new version of LAEP.

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MAEP(Metagenomics Assembly Evaluation Pipeline)

E-mail: liaoherui@mail.dlut.edu.cn

Version: V3.0

This is not a production-ready software repository and is still under active development. Bugs and feature requests will not addressed. Note:MAEP can only be used on KMBGI's server.It will be updated to run on other servers soon after

Abstract

MAEP is a new version of LAEP and can be used to evaluate the assembly quality of metagenomics data(especially from the different sequencing platforms and different assembly strategies).By the way ,this pipeline can support multiple samples parallel evaluation.

The program is broken down into several module:

  • Module 1: Assess contig/scaffold quality with Quast v5.0.0
  • Module 2: Binning contig/scaffold with MaxBin 2.2.4
  • Module 3: Map raw reads to contig/assembly and calculate the map rate with BWA 0.7.17
  • Module 4: Evaluate the bins generated by Maxbin and output the bin table.
    ( Please note that this module will use Checkm v1.0.12(Assess bins quality),Quast v5.0.0(Assess bin quality), Kraken 0.10.6(Annotation),Aragorn v1.2.38, Barrnap 0.9,Prodigal v2.6.3(These three tools are used to annotate RNA info) )
  • Module 5: Plot according to the bin table.

Manuals

  • Quick Start:
    python Lazy_MAEP.py -l list/contig_raw_reads.list -s list/sample.list -o zxy_p4_test
    By the way,you can put this command into a bash script and use it.
  • Option Illustration:

-l :
This option refers to the input list.The list (tab seperated) is composed of 4 parts.
column 1: sample name
column 2: prefix (Usuallly refer to different sequencing platforms or assembly strtegies)
column 3: assembly result dir(.fasta file with multi contigs/scaffolds)
column 4 and column 5: PE raw reads dir
Example List:(One sample ,two sequencing platforms) 

zxy Athena_10X  /mnt/10X_athena.fasta /mnt/osf1/zxy_10X_R1.fq.gz  /mnt/osf1/zxy_10X_R2.fq.gz 
zxy Illumina /mnt/pacbio_flye.fasta  /mnt/osf1/zxy_1.fq.gz /mnt/osf1/zxy_2.fq.gz

-s :
This option refers to the sample name list.For example,if your input data only refers to one sample(suppose the sample name is 'zxy'), then your sample list should be:

zxy

Or, you have two samples(zxy and hlj),then,your list should be:

zxy
hlj

,more samples' condition is similar.

-o :
This option means output dir.

Output

There are two parts of output.One is report(.html),another is literature figure.
The results can be downloaded in Report folder(.html) or Figure folder(literature figure)