MAGs-pipeline

This website contains the MAG construction pipeline for RMGMC Metagenome Project. <<<<<<< HEAD

Including:

======= Including:

1e71593615c3955e766a52a43875c2a0ba6511ea (1) Reads quality control and low-quality reads timming

(2) metagenome assembly using two tools

(3) merge multiple sources of assembles

(4) SNP, Indels correction by re-sequencing methods

(5) MAGs construction by metabat2, maxbin and concoct

(6) Integrating MAGs by DAStools

(7) MAGs quality control and dereplication

(8) Taxonomy identification

(9) maximum-likelihood tree construction based on MAGs <<<<<<< HEAD

1. Package Required

   (1) Trimmomatic(v.0.33), http://www.usadellab.org/cms/index.php?page=trimmomatic

   (2) BWA(v.0.7.17), https://github.com/lh3/bwa

   (3) MEGAHIT(v.1.1.1), https://github.com/voutcn/megahit

   (4) IDBA-UD(v.1.1.3), https://www.psc.edu/user-resources/software/idba-ud

   (5) AMOS(v.3.1.0), http://amos.sourceforge.net/wiki/index.php/AMOS

   (6) SAMtools(v.1.9), http://samtools.sourceforge.net/

   (7) MaxBin(v.2.2.4, under metaWRAP)

   (8) MetaBAT2(v.2.11.1 under metaWRAP)

   (9) CONCOCT(v.0.4.0 under metaWRAP)

   (10) DAS Tool(v.1.1.1), https://github.com/cmks/DAS_Tool

   (11) CheckM(v.1.0.7 under metaWRAP)

   (12) metaWRAP(v.1.3), https://github.com/bxlab/metaWRAP

   (13) GTDB-Tk(v.0.1.6), https://ecogenomics.github.io/GTDBTk

   (14) PhyloPhlAn(v.1.0), http://segatalab.cibio.unitn.it/tools/phylophlan/

   (15) Prodigal(v.2.6.3), https://github.com/hyattpd/Prodigal

2. Step1: shell script generation

   Use Yak metagenome data as an example.

   perl Meta-Pipeline.pl -fqlist Yak-fqlist.txt -host a -set Yak-Group.txt

3. Step2: run pipeline (fold shell/)

   S1.QC*sh: Reads quality control and remove host genomes

   S2.idba*sh: IDBA assembly

   S2.megahit*sh: MEGAHIT assembly

   S3.merge*sh: merge two assemble results from above two steps

   S4.correct1(2).sh: contigs correction

   S5.BIN*sh: run metabat2 as the first binning methods

   S6.predictsh & S7.GeneSetsh: used in RMGMC geneset

   S8.Abund.*sh: gene abundance calculation

4. Step3: run DAStools to improve the MAG quality and quantity

   perl Meta-DAStool.pl -input Yak-metabat2.list

   scripts will be generated in shell/ and run all scripts simultaneously

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