基因组共线用Mauve

文献信息
标题：Mauve: multiple alignment of conserved genomic sequence with rearrangements
中文：保守基因组序列重排多重比对
杂志：GENOME RESEARCH
时间：2004
引用：3291

官网：https://asap.genetics.wisc.edu/
GITHUB: https://github.com/koadman/mauve
Third parter: http://darlinglab.org/mauve/mauve.html
Manual：http://darlinglab.org/mauve/user-guide/files.html

升级版：
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. plos one 2010

1 Mavue和progressiveMauve获取

conda activate phyml
conda install progressiveMauve
conda install mauve
progressiveMauve --version
# progressiveMauve  build date Mar 27 2021 at 23:55:26

2 Mauve根据参考重排基因组

Manual: http://darlinglab.org/mauve/user-guide/reordering.html

Mauve Contig Mover (MCM)根据参考基因组reorder草图基因组，可帮助发现草图基因组的rearrangement。

java文件路径：/miniconda3/envs/phyml/share/mauve-2.4.0.snapshot_2015_02_13-4/Mauve.jar

java -Xmx500m -cp /hwfssz1/ST_HEALTH/P18Z10200N0423/hutongyuan/softwares/miniconda3/envs/phyml/share/mauve-2.4.0.snapshot_2015_02_13-4/Mauve.jar /
org.gel.mauve.contigs.ContigOrderer /
-output ./reorder/ /
-ref ./input/MF3KT15004.gbk /
-draft ./input/BF3KT15003B.fna

依次产生四个结果文件

3 mauveAligner对齐基因组

输入需要Sorted Mer List (SML)，直接用progressiveMauve生成的即可。

mauveAligner /
--output=./mauvealign/three /
--output-alignment=./mauvealign/three_align /
./input/BF3KT15003B.gbk ./input/BF3KT15003B.gbk.sslist /
./input/MF3KT15004.gbk ./input/MF3KT15004.gbk.sslist /
./input/PF3KT15003.gbk ./input/PF3KT15003.gbk.sslist

结果同progressiveMauve的xmfa

> 1:1-47420 + ./input/BF3KT15003B.gbk
> 2:97850-145094 + ./input/MF3KT15004.gbk
> 3:1711640-1758872 + ./input/PF3KT15003.gbk
=
> 1:47440-47499 + ./input/BF3KT15003B.gbk
> 2:145114-145173 + ./input/MF3KT15004.gbk
> 3:1711574-1711633 + ./input/PF3KT15003.gbk
=

4 progressiveMauve比对三个基因组

参数：
--output-guide-tree= Write out the guide tree used for alignment to a file

输出共线结果

# example_1
progressiveMauve --output=./example_1/threeway.xmfa /
./input/BF3KT15003B.gbk /
./input/MF3KT15004.gbk /
./input/PF3KT15003.gbk

xmfa文件格式
eXtended Multi-FastA (XMFA)
格式说明：http://darlinglab.org/mauve/user-guide/files.html

> 1:405-47558 + ./input/BF3KT15003B.gbk
> 2:97847-145232 + ./input/MF3KT15004.gbk
> 3:1711637-1758839 + ./input/PF3KT15003.gbk
=
> 1:47616-78246 + ./input/BF3KT15003B.gbk
> 2:145290-175920 + ./input/MF3KT15004.gbk
> 3:1888102-1918406 + ./input/PF3KT15003.gbk
=
...
> 1:1-404 + ./input/BF3KT15003B.gbk
> 1:47559-47615 + ./input/BF3KT15003B.gbk
> 2:1-2 + ./input/MF3KT15004.gbk
> 2:97842-97846 + ./input/MF3KT15004.gbk
> 3:747731-748023 + ./input/PF3KT15003.gbk
> 3:749647-749648 + ./input/PF3KT15003.gbk

输出guide tree

# example_2
progressiveMauve --output=./example_2/threeway.xmfa /
--output-guide-tree=./example_2/threeway.tree /
--backbone-output=./example_2/threeway.backbone /
./input/BF3KT15003B.gbk /
./input/MF3KT15004.gbk /
./input/PF3KT15003.gbk

5 Mauve从xmfa中获取snp

java -cp /hwfssz1/ST_HEALTH/P18Z10200N0423/hutongyuan/softwares/miniconda3/envs/phyml/share/mauve-2.4.0.snapshot_2015_02_13-4/Mauve.jar org.gel.mauve.analysis.SnpExporter /
-f threeway.xmfa /
-o threeway.snps

结果：

SNP pattern     sequence_1_Contig       sequence_1_PosInContg   sequence_1_GenWidePos1     sequence_2_Contig       sequence_2_PosInContg   sequence_2_GenWidePos2  sequence_3_Contig  sequence_3_PosInContg   sequence_3_GenWidePos3
ccn     [1,2207046]     934     934     [1,2208487]     98783   98783   [1,2208207]1712573 1712573
ttn     [1,2207046]     935     935     [1,2208487]     98784   98784   [1,2208207]1712574 1712574
ttn     [1,2207046]     936     936     [1,2208487]     98785   98785   [1,2208207]1712575 1712575

引用文章

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa. BMC Genomics. 2018

针对一个模板基因组，进行多基因组序列比较

这似乎是win版本的

更多：
一文教会您系列之 - 基因组共线性分析（Mauve）

Aligning Bacterial Genomes with Mauve
全基因组测序 从头测序(de novo sequencing) 重测序(re-sequencing)
Mauve - SNP extraction from command line