NOVOPlasty 是一個(gè)perl腳本晚吞，沒有依賴任何其他軟件转捕，下載好以后直接可以使用饭入。
下載鏈接
https://github.com/ndierckx/NOVOPlasty
其基本使用方法是
perl NOVOPlasty3.7.2.pl -c config.txt
config.txt文件是需要我們自己準(zhǔn)備的各吨，軟件包里提供了這個(gè)文件，我們需要對(duì)應(yīng)著改里面的內(nèi)容沦寂，文件的內(nèi)容如下：
Project:
-----------------------
Project name = Test
Type = mito
Genome Range = 12000-22000
K-mer = 39
Max memory =
Extended log = 0
Save assembled reads = no
Seed Input = /path/to/seed_file/Seed.fasta
Reference sequence = /path/to/reference_file/reference.fasta (optional)
Variance detection =
Chloroplast sequence = /path/to/chloroplast_file/chloroplast.fasta (only for "mito_plant" option)
Dataset 1:
-----------------------
Read Length = 151
Insert size = 300
Platform = illumina
Single/Paired = PE
Combined reads =
Forward reads = /path/to/reads/reads_1.fastq
Reverse reads = /path/to/reads/reads_2.fastq
Heteroplasmy:
-----------------------
MAF =
HP exclude list =
PCR-free =
Optional:
-----------------------
Insert size auto = yes
Insert Range = 1.9
Insert Range strict = 1.3
Use Quality Scores = no
Project:
-----------------------
Project name = Choose a name for your project, it will be used for the output files.
Type = (chloro/mito/mito_plant) "chloro" for chloroplast assembly, "mito" for mitochondrial assembly and
"mito_plant" for mitochondrial assembly in plants.
Genome Range = (minimum genome size-maximum genome size) The expected genome size range of the genome.
Default value for mito: 12000-20000 / Default value for chloro: 120000-200000
If the expected size is know, you can lower the range, this can be useful when there is a repetitive
region, what could lead to a premature circularization of the genome.
K-mer = (integer) This is the length of the overlap between matching reads (Default: 33).
If reads are shorter then 90 bp or you have low coverage data, this value should be decreased down to
23.
For reads longer then 101 bp, this value can be increased, but this is not necessary.
Max memory = You can choose a max memory usage, suitable to automatically subsample the data or when you have
limited
memory capacity. If you have sufficient memory, leave it blank, else write your available memory in GB
(if you have for example a 8 GB RAM laptop, put down 7 or 7.5 (don't add the unit in the config file))
Extended log = Prints out a very extensive log, could be useful to send me when there is a problem (0/1).
Save assembled reads = All the reads used for the assembly will be stored in seperate files; if option 2 is used, the
original ids will be retained (yes/no/2)
Seed Input = The path to the file that contains the seed sequence.
Reference (optional) = If a reference is available, you can give here the path to the fasta file.
The assembly will still be de novo, but references of the same genus can be used as a guide to resolve
duplicated regions in the plant mitochondria or the inverted repeat in the chloroplast.
References from different genus haven't beeen tested yet.
Variance detection = If you select yes, you should also have a reference sequence (previous line). It will create a vcf
file with all the variances compared to the give reference (yes/no)
Chloroplast sequence = The path to the file that contains the chloroplast sequence (Only for mito_plant mode).
You have to assemble the chloroplast before you assemble the mitochondria of plants!
Dataset 1:
-----------------------
Read Length = The read length of your reads.
Insert size = Total insert size of your paired end reads, it doesn't have to be accurate but should be close enough.
Platform = illumina/ion - The performance on Ion Torrent data is significantly lower
Single/Paired = PE/SE
Combined reads = The path to the file that contains the combined reads (forward and reverse in 1 file)
Forward reads = The path to the file that contains the forward reads (not necessary when there is a merged file)
Reverse reads = The path to the file that contains the reverse reads (not necessary when there is a merged file)
Heteroplasmy:
-----------------------
MAF = (0.007-0.49) Minor Allele Frequency: If you want to detect heteroplasmy, first assemble the genome
without this option. Then give the resulting sequence as a reference and as a seed input. And give the
minimum minor allele frequency for this option (0.01 will detect heteroplasmy of >1%)
HP exclude list = Option not yet available
PCR-free = (yes/no) If you have a PCR-free library write yes
Optional:
-----------------------
Insert size auto = (yes/no) This will finetune your insert size automatically (Default: yes)
Insert Range = This variation on the insert size, could lower it when the coverage is very high or raise it when the
coverage is too low (Default: 1.9).
Insert Range strict = Strict variation to resolve repetitive regions (Default: 1.3).
Use Quality Scores = It will take in account the quality scores, only use this when reads have low quality, like with the
300 bp reads of Illumina (yes/no)
我們自己需要修改的包括：
Project name:給自己的項(xiàng)目起一個(gè)名字学密，自己可以隨便起
Type: 如果是組裝葉綠體需要將這一項(xiàng)改為 chloro
Genome Range:葉綠體基因組序列長度通常為150kb左右，這一項(xiàng)可以改為130,000-170,000
K-mer：一般直接用默認(rèn)的39即可
Max memory：Extended log：這兩項(xiàng)不用管
Save assembled reads：這一項(xiàng)如果改為yes的話會(huì)將用于組裝的數(shù)據(jù)以fasta的格式保留下來传藏。
Seed Input：種子序列的路徑腻暮，軟件包里提供了一個(gè)Seed_RUBP_cp.fasta文件，直接使用這個(gè)文件就可以
Reference sequence：參考序列的路徑漩氨，這個(gè)參考序列是可選的西壮，如果沒有參考序列，等號(hào)后面的內(nèi)容需要?jiǎng)h除
Variance detection：這個(gè)不用管叫惊，直接空著就可以
Chloroplast sequence：組裝葉綠體的時(shí)候需要把等號(hào)后面的內(nèi)容刪掉
Read Length Insert size Platform：這些可以在測(cè)序報(bào)告中找到款青，需要改為自己的
Single/Paired:好像只支持雙端測(cè)序數(shù)據(jù)
Combined reads：這個(gè)可以不用管
Forward reads：第一個(gè)fastq文件的路徑
Reverse reads：第二個(gè)fastq文件的路徑
剩下的都可以不用管了
這個(gè)config.txt文件準(zhǔn)備好就可以直接運(yùn)行
perl NOVOPlasty3.7.2.pl -c config.txt
軟件運(yùn)行很快，不一會(huì)就可以拿到自己的結(jié)果了霍狰！
歡迎關(guān)注我的公眾號(hào)
小明的數(shù)據(jù)分析筆記本
公眾號(hào)二維碼.jpg
