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 <parameters>
  -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 <parameters>
  -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 <parameters>  -h, --help            show this help message and exit  -i GENOME             (*Required) Genome file to be identified, FASTA format.  -c {plant,animal,other}                        Specify clade of this genome. Plant will search TTTAGGG, animal will search TTAGGG, other will use tidk explore's                       suggestion, default: other  -m MIN_REPEAT_TIMES   The min repeat times to be reported, default: 100  -p PREFIX             The prefix used on generated files, default: quarTeT
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 <parameters>
  -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: <match> <mismatch> <delta> <PM> <PI> <minscore> Default: 2 7 7 80 10 50
  --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