Checkm 1.4GB binning, bin_refinement, reassemble_bins KRAKEN 192GB kraken NCBI_nt 99GB blobology, classify_bins NCBI_tax 283MB blobology, classify_bins Indexed hg38 34GB read_qc 这里我们安装数据库到~/db目录,保证你有权限,但要保证至少有500GB的空间。请根据你的情况修改为自己有权限且空间足够的...
reassemble_bins 分箱重组装模块,该模块根据分箱结果bin,将短序列reads重新组装,以期优化组装结果。 quant_bins 分箱丰度分析模块。 kraken2 短序列reads/重叠群contigs分类学注释模块。 blobology 数据可视化模块。 annotate_bins 分箱基因功能注释模块。 classfy_bins 分箱分类学注释模块。 步骤一:read_qc 高通量测...
metawrap reassemble_bins -o BIN_REASSEMBLY -1 CLEAN_READS/ALL_READS_1.fastq -2 CLEAN_READS/ALL_READS_2.fastq -t 8 -m 800 -c 50 -x 10 -b BIN_REFINEMENT/metaWRAP_bins 结果统计见BIN_REASSEMBLY/reassembled_bins.stats,发现3个bin通过严格模式下得到优化,6个通过宽松模式得到改进,4个没有变化。
#该路径下这3个脚本都用到checkM,都需要改默认的--tmpdir cd/opt/conda/envs/metawrap-env/bin/metawrap-modulesgrepcheckm *sh|awk-F":"'{print $1}'|sort|uniqbin_refinement.shbinning.shreassemble_bins.sh#以binning.sh为例 #在checkm命令前加一行,新建一个较短的tmp目录,用于存放checkM的tmp文件mkdir-...
reassemble_bins 重装分箱Reassemble bins using metagenomic reads quant_bins 定量Quantify the abundance of each bin across samples blobology 可视化Blobology module kraken 物种注释KRAKEN module 想查看每个模块的具体参数,如组装metawrap assembly -h Usage: metawrap assembly [options] -1 reads_1.fastq -2 re...
重组装Reassemble_bins:利用原始序列和评估软件二次组装,改善Bin的N50、完整度4) 定量Quant_bins: 估计样品中每个bin的丰度并热图展示 气泡图Blobology: blobplots可视化群体的contigs的物种和Bin分布 物种注释Classify_bins: 对Bin物种注释 基因注释Annotate_bins: 预测Bin中的基因 ...
metawrap reassemble_bins -o BIN_REASSEMBLY -1 CLEAN_READS/ALL_READS_1.fastq -2 CLEAN_READS/ALL_READS_2.fastq -t 8 -m 800 -c 50 -x 10 -b BIN_REFINEMENT/metaWRAP_bins 结果统计见BIN_REASSEMBLY/reassembled_bins.stats,发现3个bin通过严格模式下得到优化,6个通过宽松模式得到改进,4个没有变化。
MetaWRAP-Reassemble_bins can then be used to reassemble the reads belonging to each bin, improving their N50, completion, and contamination. The resulting bins can be visualized by using the metaWRAP-Blobology module [39], which plots the contigs of the joint assembly on a blob plot, ...
使用metaWRAP的Reassemble_bins模块对原始bins进行二次组装。仅展示CheckM估计完整度大于50%,污染率小于10%的bins 图6. 水体、肠道和土壤中高纯度bins(污染率<5%)分别在完整度70%、80%、90%、95%下的数量 MetaWRAP运行在不同最小完整度参数下的结果。 图7. Blobology模块可视化水体、肠道和土壤宏基因组拼接叠连...
while also proving metrics of their completion and contamination. MetaWRAP-Reassemble_bins can then be used to reassemble the reads belonging to each bin, improving their N50, completion, and contamination. The resulting bins can be visualized by using the metaWRAP-Blobology module [39], which plo...