下载数据库

下载 CheckM 数据库：

mkdir MY_CHECKM_FOLDER
# Now manually download the database:
cd MY_CHECKM_FOLDER
wget <https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz>
tar -xvf *.tar.gz
rm *.gz
cd ../

下载KRAKEN2标准数据库：

##下载kraken2
<https://github.com/DerrickWood/kraken2>
##数据库
kraken2-build --standard --threads 24 --db MY_KRAKEN2_DB

KRAKEN2

mkdir database

kraken2-build --download-taxonomy --db database

kraken2-build --download-library bacteria --db database

kraken2-build --build --db database

##运行
kraken2 --db database --report k2_report.txt --report-minimizer-data \\
    --output k2_output.txt /home/liuli/meta/out_lh/assembly.fasta

Downloading the NCBI_nt BLAST database:

for i in {00..90}
do
  wget -c --no-check-certificate <ftp://download.nmdc.cn/tools/meta/NCBI/nt/nt.$i.tar.gz> || echo "Failed to download nt.$i.tar.gz"
done

去除宿主基因组

##hg38.fa为宿主基因组

bmtool -d hg38.fa -o hg38.bitmask
srprism mkindex -i hg38.fa -o hg38.srprism -M 100000
ftps://download.nmdc.cn/tools/meta/kraken2/k2_pluspfp_20230314.tar.gz

最后配置config-metawrap文件

# Paths to metaWRAP scripts (dont have to modify)
mw_path=$(which metawrap)
bin_path=${mw_path%/*}
SOFT=${bin_path}/metawrap-scripts
PIPES=${bin_path}/metawrap-modules

# CONFIGURABLE PATHS FOR DATABASES (see 'Databases' section of metaWRAP README for details)
# path to kraken standard database
KRAKEN2_DB=~/last

# path to indexed human (or other host) genome (see metaWRAP website for guide). This includes .bitmask and .srprism files
BMTAGGER_DB=/home/liuli/liuli/liuli/meta/metaWRAP-master/human

# paths to BLAST databases
BLASTDB=/home/liuli/liuli/liuli/meta/metaWRAP-master/NCBI_nt
TAXDUMP=/home/liuli/liuli/liuli/meta/metaWRAP-master/NCBI_tax

运行 metaWRAP-Read_qc 来修剪读取并消除人为污染

metawrap read_qc -1 /home/liuli/liuli/liuli/meta/illumiona/clean/L1EHK3003588-LH_meta1_1.fastq  \\
                 -2 /home/liuli/liuli/liuli/meta/illumiona/clean/L1EHK3003588-LH_meta1_2.fastq  \\
                  -t 24 -o READ_QC

组装，一般使用spades，建议使用最新版

Kraken 分类

metawrap kraken2 -t 96  -o output_dir  \\
cleanSPAdes_retry/scaffolds.fasta  \\
./READ_QC/final_pure_reads_1.fastq ./READ_QC/final_pure_reads_2.fastq