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https://github.com/franciscozorrilla/metaGEM A Snakemake-based workflow to generate high quality metagenome assembled genomes from short read paired-end data, reconstruct genome scale metabolic models, and perform community metabolic interaction simulations on high performance computing clusters.[……] […] 链接：https://www.jianshu.com/p/cceeb7d1f413来源软件安装 如果要顺利运行程序，要求JAVA > 1.7, 以及根据基因组大小而定的内存，一般而言是1M大小的基因对应1GB的内存。
总览Pilon有如下作用
他以FASTA和BAM文件作为输入，根据比对结果对输入的参考基因组进行提高，包括
[…] Three easy ways to download multiple sequences from NCBI There are different ways of how to download multiple sequences from the NCBI databases in a single request. 1) Using the batch Entrez website
http://www.>ncbi.nlm.nih.gov/sites/batchentrez 2) Using Perl: (cop[……] […] 链接：https://www.jianshu.com/p/175c3282a61c BBMap/BBTools是一种用于DNA和RNA测序reads的拼接感知全局的比对工具。它可以处理的reads包括，Illumina，454，Sanger，Ion Torrent，Pac Bio和Nanopore。 BBMap快速且极其准确，特别是对于高度突变的基因组或长插入读数，甚至超过100kbp长的全基因缺失。它对基因组大小或contigs数量没有上限。并且已经成功地用于绘制到具有超过2亿个contigs的85gb的土壤宏基因组。此外，与其他比对工具相比，索引阶段非常快。 BBMap[……]
[…] https://bioinformatics.stackexchange.com/questions/2341/how-to-extract-convert-gff3-cds-sequences-to-multifasta
Using python and this GFF parser that mimics Biopython’s SeqIO parsers:
[…] #!/bin/bash #PBS -l walltime=48:00:00,nodes=8:ppn=4 #PBS -N bbmap_batch #PBS -l walltime=48:00:00 #megahit -1 /disk/rdisk09/zhiyshen/combined_HKG_1.fastq.gz -2 /disk/rdisk09/zhiyshen/combined_HKG_2.fastq.gz -m 0.9 -o /disk/rdisk09/zhiyshen/HKG_coassembly_out –min-contig-len 2000 -t 28 source a[……] […] data<-read.table("fastani_matrix.txt", header=TRUE )
(base) zyshen@wyq-P310:~/work/deltaBS/fastaANI$ more fastani_matrix.txt B1147 E4385 E4742 E4930 EC5350 ROAR019 B1147 100 94.681488 94.696358 94.648102 99.785301 94.803284 E4385 94.681488 100 96.50248 97.408295 94.496964 95.691849 E[……] […] https://github.com/LangilleLab/microbiome_helper/wiki/Metagenomics-Tutorial-(Humann2) […] http://www.360doc.com/content/20/0823/10/71250389_931761136.shtml https://github.com/LangilleLab/microbiome_helper/wiki/Metagenomics-standard-operating-procedure-v2 Note that this workflow is continually being updated. If you want to use the below commands be sure to keep track of them locally[……] […] |
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