手动安装MetaWRAP
依赖软件安装--apt安装
sudo -i
apt update
## blast+
apt install ncbi-blast+
## bowtie
apt install bowtie
## bwa
apt install bwa
## fastqc
apt install fastqc ##自动安装了一堆东西
## perl
apt install perl
## R & ggplot2
apt install r-base ##又安装了一大堆
R
install.packages("ggplot2") ##需要点时间
q()
n
## samtools
apt install samtools
## spades
apt install spades
## salmon
apt install salmon
## seaborn
pip install statsmodels seaborn
需要手动安装的软件
## MegaHit
apt install g++ zlib1g-dev git
mkdir software ; cd software
git clone https://github.com/voutcn/megahit.git
cd megahit
make
cp megahit megahit_asm_core megahit_sdbg_build megahit_toolkit /usr/local/bin/
## prokka
apt install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl ##相当多的东西，中间需要按一次回车
cpan Bio::Perl
wget http://www.vicbioinformatics.com/prokka-1.12.tar.gz
tar -zxvf prokka-1.12.tar.gz
cd prokka-1.12/bin
./prokka --setupdb
cp prokka prokka-build_kingdom_dbs prokka-clusters_to_hmm prokka-genpept_to_fasta_db prokka-make_tarball prokka-uniprot_to_fasta_db prokka-biocyc_to_fasta_db prokka-cdd_to_hmm prokka-genbank_to_fasta_db prokka-hamap_to_hmm prokka-tigrfams_to_hmm /usr/local/bin/
## maxbin2
cd /home/llt/software
wget https://downloads.jbei.org/data/microbial_communities/MaxBin/getfile.php?MaxBin-2.2.6.tar.gz
mv 'getfile.php?MaxBin-2.2.6.tar.gz' MaxBin-2.2.6.tar.gz
tar -zxvf MaxBin-2.2.6.tar.gz
cd MaxBin-2.2.6/src
make
cd ..
./autobuild_auxiliary
## metaBAT
apt install libboost-dev scons
wget https://bitbucket.org/berkeleylab/metabat/downloads/metabat-static-binary-linux-x64_v2.12.1.tar.gz
tar xzvf metabat-static-binary-linux-x64_v2.12.1.tar.gz
cd metabat
cp contigOverlaps metabat metabat1 metabat2 jgi_summarize_bam_contig_depths /usr/local/bin/
##concoct
apt install libgsl0-dev picard-tools bowtie2 parallel python-pip
pip install cython biopython pandas scikit-learn nose
wget https://github.com/BinPro/CONCOCT/archive/1.0.0.zip
unzip 1.0.0.zip
cd CONCOCT-1.0.0/
python setup.py install
## quast
wget https://github.com/ablab/quast/releases/download/quast_5.0.2/quast-5.0.2.tar.gz
tar -zxvf quast-5.0.2.tar.gz
cd quast-5.0.2/
./setup.py install_full
## checkM
apt install prodigal
wget https://github.com/matsen/pplacer/releases/download/v1.1.alpha17/pplacer-Linux-v1.1.alpha17.zip
unzip pplacer-Linux-v1.1.alpha17.zip
cd pplacer-Linux-v1.1.alpha17/
cp guppy pplacer rppr /usr/local/bin/
sudo pip install numpy checkm-genome
checkm
/mnt/d/linux/database/checkm
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
tar zxf checkm_data_2015_01_16.tar.gz
## KronaTools
git clone https://github.com/marbl/Krona.git
cd Krona/KronaTools/
mkdir /mnt/d/linux/database/krona
mkdir /mnt/d/linux/database/krona/taxonomy
sudo ./install.pl --taxonomy /mnt/d/linux/database/krona/taxonomy
./updateTaxonomy.sh
./updateAccessions.sh
## trim_galore
apt install cutadapt
curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.4.5.tar.gz -o trim_galore.tar.gz
tar xvzf trim_galore.tar.gz
cd TrimGalore-0.4.5/
cp trim_galore /usr/local/bin/
## taxator-tk
apt install cmake libboost-all-dev
git clone https://github.com/fungs/taxator-tk.git
cd taxator-tk/
./build.sh
cd Build-x86_64/
cp alignments-filter binner taxator taxknife unittest_ncbitaxonomy /usr/local/bin/
安装完后，添加maxbin和quast软件的路径到path
安装MetaWRAP
git clone https://github.com/bxlab/metaWRAP.git
##下载后添加/home/llt/software/metaWRAP/bin 到path
MetaWRAP使用
Step 1: Run metaWRAP-Read_qc to trim the reads and remove human contamination
cat GCF_001650195.1_ASM165019v1_genomic.fna GCF_000723405.1_HINTER_V1_genomic.fna GCF_000697965.2_ASM69796v2_genomic.fna GCF_000420025.1_ASM42002v1_genomic.fna GCF_000317105.1_ASM31710v1_genomic.fna GCF_000203835.1_ASM20383v1_genomic.fna GCF_000164985.3_ASM16498v2_genomic.fna GCF_000143145.1_ASM14314v1_genomic.fna GCF_000092865.1_ASM9286v1_genomic.fna GCF_000024985.1_ASM2498v1_genomic.fna GCF_000021345.1_ASM2134v1_genomic.fna GCF_000020025.1_ASM2002v1_genomic.fna GCF_000016765.1_ASM1676v1_genomic.fna GCF_000014185.1_ASM1418v1_genomic.fna GCF_000011365.1_ASM1136v1_genomic.fna GCF_000010625.1_ASM1062v1_genomic.fna GCF_000007825.1_ASM782v1_genomic.fna GCF_000006965.1_ASM696v1_genomic.fna GCF_000006765.1_ASM676v1_genomic.fna GCF_900104745.1_IMG-taxon_2636416006_annotated_assembly_genomic.fna > removed.fna
cp /home/llt/remove_test/ASM/removed.fna /home/llt/database/removed/
bmtool -d removed.fna -o hg38.bitmask
srprism mkindex -i removed_1-50.fna -o hg38.srprism -M 10000
metawrap read_qc -1 /home/llt/remove_test/ssg1_10m_1.fastq -2 /home/llt/remove_test/ssg1_10m_2.fastq -t 8 -o READ_QC/ --skip-trimming --skip-pre-qc-report
Step 2: Assembling the metagenomes with the metaWRAP-Assembly module
##使用metaspades拼接
metawrap assembly -1 /mnt/d/linux/experiment/data/clean/trim_strict/2m/ssg1_2m.1.fq -2 /mnt/d/linux/experiment/data/clean/trim_strict/2m/ssg1_2m.2.fq -m 200 -t 4 --metaspades -o ASSEMBLY
Step 3: Run Kraken module on both reads and the assembly
Step 4: Bin the co-assembly with three different algorithms with the Binning module
metawrap binning -o INITIAL_BINNING -t 8 -a contigs.fasta --metabat2 --maxbin2 --concoct --universal ssg1_10m_1.fastq ssg1_10m_2.fastq
Step 5: Consolidate bin sets with the Bin_refinement module
metawrap bin_refinement -o BIN_REFINEMENT -t 8 -m 13 -A INITIAL_BINNING/metabat2_bins/ -B INITIAL_BINNING/maxbin2_bins/ --quick
Step 6: Visualize the community and the extracted bins with the Blobology module
metawrap blobology -a contigs.fasta -t 8 -o BLOBOLOGY --bins BIN_REFINEMENT/metawrap_bins ssg1_10m_1.fastq ssg1_10m_2.fastq
Step 7: Find the abundaces of the draft genomes (bins) across the samples
Step 8: Re-assemble the consolidated bin set with the Reassemble_bins module
metawrap reassemble_bins -o BIN_REASSEMBLY -1 ssg1_10m_1.fastq -2 ssg1_10m_2.fastq -t 8 -m 13 -b BIN_REFINEMENT/metawrap_bins --skip-checkm
Step 9: Determine the taxonomy of each bin with the Classify_bins module
metawrap classify_bins -b BIN_REASSEMBLY/reassembled_bins -o BIN_CLASSIFICATION -t 8
Step 10: Functionally annotate bins with the Annotate_bins module
metaWRAP annotate_bins -o FUNCT_ANNOT -t 8 -b BIN_REASSEMBLY/reassembled_bins/