功能
参考引导的基因组组装
1.AssemblyMapper: reference-guided genome assembly
基于长读长的填缝
2.GapFiller: long-reads based gap filling
端粒识别
3.TeloExplorer: telomere identification
着丝粒候选预测
4.CentroMiner: centromere candidate prediction
1、软件安装
git clone https://github.com/aaranyue/quarTeT.git
cd quarTeT && chmod 755 *
2、软件依赖
#trf手动安装(添加路劲到.bashrc)
wget https://github.com/Benson-Genomics-Lab/TRF/archive/master.zip
mv master.zip trf.zip
unzip trf.zip && cd TRF-master/
./configure --prefix=/path/you/TRF
make && make install
#trf conda安装
conda install trf -y
#tidy conda安装
conda install -c bioconda tidk -y
#Minimap2
conda install -c "bioconda/label/cf201901" minimap2
#MUMmer4
git clone https://github.com/mummer4/mummer.git
cd mummer
./configure --prefix=/path/to/installation
make
make install
#gnuplot推荐conda安装（会添加很多其他依赖）
conda install -c "bioconda/label/cf201901" gnuplot
#EDTA手动安装或conda安装
git clone https://github.com/oushujun/EDTA.git
conda env create -f EDTA.yml
conda activate EDTA
perl EDTA.pl
#R和Python3一般服务器上都会配置
3、软件的使用
AssemblyMapper
#{prefix}.bp.hap1.p_ctg.gfa 和{prefix}.bp.hap2.p_ctg.gfa转换为fasta格式作为输入文件
Usage: python3 quartet.py AssemblyMapper
-h, --help show this help message and exit
-r REFERENCE_GENOME (*Required) Reference genome file, FASTA format.
-q CONTIGS
(*Required) Phased contigs file, FASTA format.
-c MIN_CONTIG_LENGTH Contigs shorter than INT (bp) will be removed, default: 50000
-l MIN_ALIGNMENT_LENGTH
The min alignment length to be select (bp), default: 10000
-i MIN_ALIGNMENT_IDENTITY
The min alignment identity to be select (%), default: 90
-p PREFIX The prefix used on generated files, default: quarTeT
-t THREADS Use number of threads, default: 1
-a {minimap2,mummer} Specify alignment program (support minimap2 and mummer), default: minimap2
--plot Plot a colinearity graph for draft genome to reference alignments. (will cost more time)
--overwrite Overwrite existing alignment file instead of reuse.
--minimapoption MINIMAPOPTION
Pass additional parameters to minimap2 program, default: -x asm5
--nucmeroption NUCMEROPTION
Pass additional parameters to nucmer program.
--deltafilteroption DELTAFILTEROPTION
Pass additional parameters to delta-filter program.
#输出文件为：
{prefix}.draftgenome.fasta | The pseudo-chromosome-level assembly, fasta format.
{prefix}.draftgenome.agp | The structure of this assembly, AGP format.
{prefix}.draftgenome.stat | The statistic of this assembly, including total size and each chromosome's size, GC content, gap count and locations.
{prefix}.draftgenome.png | The figure draws relative length of chromosomes and gap locations for assembly.
{prefix}.contig.mapinfo | The statistic of input contigs, including total mapped and discarded size, and each contig's destination.
{prefix}.contig_map_ref.png | The alignment colinearity graph between contigs and reference genome.
{prefix}.draftgenome_map_ref.png | The alignment colinearity graph between this assembly genome and reference genome. Only available with --plot.
GapFiller
Usage: python3 quartet.py GapFiller
-h, --help show this help message and exit
-d DRAFT_GENOME (*Required) Draft genome file to be filled, FASTA format.
-g GAPCLOSER_CONTIG [GAPCLOSER_CONTIG ...]
(*Required) All contigs files (accept multiple file) used to fill gaps, FASTA format.
-f FLANKING_LEN The flanking seq length of gap used to anchor (bp), default: 5000
-l MIN_ALIGNMENT_LENGTH
The min alignment length to be select (bp), default: 1000
-i MIN_ALIGNMENT_IDENTITY
The min alignment identity to be select (%), default: 40
-m MAX_FILLING_LEN The max sequence length acceptable to fill any gaps, default: 1000000
-p PREFIX The prefix used on generated files, default: quarTeT
-t THREADS Use number of threads, default: 1
--overwrite Overwrite existing alignment file instead of reuse.
--minimapoption MINIMAPOPTION
Pass additional parameters to minimap2 program, default: -x asm5
TeloExplorer
#需要fasta格式的基因组文件作为输入文件（为挂载到假染色体上的scaffold序列） Usage: python3 quartet.py TeloExplorer
eg：
python3 ~/biosoft/quarTeT/quartet.py TeloExplorer -i group.asm.fasta -c plant -p sx_tm
#输出文件为：
sx_tm.telo.info | The statistic of telomere, including monomer, repeat times on both end of each chromosome.
sx_tm.telo.png | The figure draws telomere location, alongside relative length of chromosomes and gap locations for assembly.
CentroMiner:
#需要fasta格式的基因组文件作为输入文件（为挂载到假染色体上的scaffold序列）
#或者，以 gff3 格式添加 TE 注释（或仅 LTR 注释）的输入可以提高性能。
#建议使用 EDTA 获取 TE 注释。
#{genome file}.mod.EDTA.TEanno.gff3 由EDTA生成，可以直接提供CentroMiner，除非您的序列ID超过15个字符。
Usage: python3 quartet.py CentroMiner
-h, --help show this help message and exit
-i GENOME_FASTA (*Required) Genome file, FASTA format.
--TE TE TE annotation file, gff3 format.
-n MIN_PERIOD Min period to be consider as centromere repeat monomer. Default: 100
-m MAX_PERIOD Max period to be consider as centromere repeat monomer. Default: 200
-s CLUSTER_IDENTITY Min identity between TR monomers to be clustered (Cannot be smaller than 0.8). Default: 0.8
-d CLUSTER_MAX_DELTA Max period delta for TR monomers in a cluster. Default: 10
-e EVALUE E-value threholds in blast. Default: 0.00001
-g MAX_GAP Max allowed gap size between two tandem repeats to be considered as in one tandem repeat region. Default: 50000
-l MIN_LENGTH Min size of tandem repeat region to be selected as candidate. Default: 100000
-t THREADS Limit number of using threads, default: 1
-p PREFIX Prefix used by generated files. Default: quarTeT
--trf [TRF_PARAMETER ...]
Change TRF parameters:
--overwrite Overwrite existing trf dat file instead of reuse.
eg: python3 ~/biosoft/quarTeT/quartet.py CentroMiner -i group.asm.fasta -p sx_cm -t 20
#输出文件为：
sx_cm.best.candidate | The best centromere candidate on each chromosome, and corresponding monomers.
sx_cm.centro.png | The figure draws best centromere candidate location, alongside relative length of chromosomes and gap locations for assembly.
candidate/ | The folder of all centromere candidates. Check here if the best candidate doesn't look well.
TRfasta/ | The folder of all tandem repeat monomers identified by trf and cluster result on each chromosome.
TRgff3/ | The folder of all tandem repeat hit by BLAST on each chromosome, in gff3 format.
后续若有报错信息，会继续更新