多基因组共线性分析-ntsynt

1.简介

ntsynt是一个用于多个全基因组比对并识别共线块的工具，它的核心思路是通过利用minimizers和graph-based方法来识别基因组间的共线块，核心步骤如下：为每个基因组生成有序的minimizers草图-->筛选出单拷贝的minimizers-->构建初始minimizer图(minimizers作为节点，基因组上相邻的minimizers作为边)-->初始minimizer图优化(移除缠结关系)-->初始共线块识别-->迭代细化(对于初始共线块中不存在的minimizers草图采用更小的minimizers生成minimizer图并简化)-->最终的共线块。
Tips：实测12个1G的基因组跑90min结束；

2.安装

conda create -n ntsynt python=3.10
conda activate ntsynt
conda install -c bioconda -c conda-forge ntsynt intervaltree pybedtools ncls python-igraph gcc meson ninja snakemake samtools seqtk btllib=1.6.2

3.输入文件

usage: ntSynt [-h] [--fastas_list FASTAS_LIST] -d DIVERGENCE [-p PREFIX] [-k K] [-w W] [-t T] [--fpr FPR] [-b BLOCK_SIZE] [--merge MERGE]
              [--w_rounds W_ROUNDS [W_ROUNDS ...]] [--indel INDEL] [-n] [--benchmark] [-f] [--dev] [-v]
              [fastas ...]

ntSynt: Multi-genome synteny detection using minimizer graphs

positional arguments:
  fastas                Input genome fasta files

optional arguments:
  -h, --help            show this help message and exit
  --fastas_list FASTAS_LIST
                        File listing input genome fasta files, one per line
  -d DIVERGENCE, --divergence DIVERGENCE
                        Approx. maximum percent sequence divergence between input genomes (Ex. -d 1 for 1% divergence).
                        This will be used to set --indel, --merge, --w_rounds, --block_size
                        See below for set values - You can also set any of those parameters yourself, which will override these settings.
  -p PREFIX, --prefix PREFIX
                        Prefix for ntSynt output files [ntSynt.k.w]
  -k K                  Minimizer k-mer size [24]
  -w W                  Minimizer window size [1000]
  -t T                  Number of threads [12]
  --fpr FPR             False positive rate for Bloom filter creation [0.025]
  -b BLOCK_SIZE, --block_size BLOCK_SIZE
                        Minimum synteny block size (bp)
  --merge MERGE         Maximum distance between collinear synteny blocks for merging (bp). 
                        Can also specify a multiple of the window size (ex. 3w)
  --w_rounds W_ROUNDS [W_ROUNDS ...]
                        List of decreasing window sizes for synteny block refinement
  --indel INDEL         Threshold for indel detection (bp)
  -n, --dry-run         Print out the commands that will be executed
  --benchmark           Store benchmarks for each step of the ntSynt pipeline
  -f, --force           Run all ntSynt steps, regardless of existing output files
  --dev                 Run in developer mode to retain intermediate files, log verbose output
  -v, --version         show program's version number and exit

运行示例：

ntSynt -d 5 assembly1.fa assembly2.fa assembly3.fa
或者
ntSynt -d 5 --fastas_list fasta_list -t 30

4.输出文件

输出文件是

python3 denovo_synteny_block_stats.py -h
usage: denovo_synteny_block_stats.py [-h] --tsv TSV --fai FAI [FAI ...]

Compute de novo stats on synteny blocks

optional arguments:
  -h, --help           show this help message and exit
  --tsv TSV            ntSynt synteny block file
  --fai FAI [FAI ...]  FAI files for the compared genomes

###下载
wget -c https://github.com/marbl/Mash/releases/download/v2.3/mash-Linux64-v2.3.tar
tar xvf mash-Linux64-v2.3.tar
###使用
mash dist -p 10 A.genome.fa B.genome.fa
###结果
reference-ID  query-ID  distance  p-value  shared-hashes
A.genome.fa  B.genome.fa  0.117785  1.05717e-96  44/1000