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=<file> 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
