git clone https://github.com/dfguan/purge_dups.git cd purge_dups/src && make Run the following commands to install runner (optional), this is only needed when you want to run scripts/run_purge_dups.py: git clone https://github.com/dfguan/runner.git cd runner && python3 setup.py ins...
网址:https://github.com/dfguan/purge_dups 介绍:purge_dups软件能根据read深度分析组装序列中haplotigs(异源二倍体)和overlaps(组装中的重复区域),以提高de novo组装的精准性。工作过程组要分为3步: (1)将用于组装的三代或者二代测序数据比对到组装结果上以计算基因组各部分覆盖度 (2)组装结果自己和自己比对...
git clone https://github.com/dfguan/purge_dups.git cd purge_dups/src && make Dependencies另外还有一个依赖软件需要安装,三代对比软件minimap2 ## minimap2自动安装conda install-c bioconda minimap2## minimap2手动安装wget https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-li...
# purge haplotigs and overlap~/opt/biosoft/purge_dups/bin/purge_dups-2-T cutoffs-c PB.base.covasm.split.self.paf.gz>dups.bed2>purge_dups.log dups.bed里的第四列就是每个contig的分类信息,分为"JUNK", "HIGHCOV", "HAPLOTIG", "PRIMARY", "REPEAT", "OVLP" 这6类,其中只有 purge_dups...
Hi, i used purge_dups to purge my assembly. And something error in calcuts process. My command as follows: minimap2 -xasm20 -t 10 -I 5 contig.fa HiFi.fq.gz | gzip -c - >HiFi_alinI.paf.gz pbcstat HiFi_alinI.paf.gz But, i could not obtain ...
Hi I found the hifiasm will purge assembly when use default -l parameter, which got the same hifiasm.p_ctg.fasta as "-l 2". And when I use default parameter to assembly, and the use 'purge_dups' purging , it still purge more. But my coll...
Hi, I keep getting a segmentation fault when running the "pbcstat" on the paf.gz file, which is a 10G file. See the following: 16:57:12 $ ~/software/purge_dups/bin/pbcstat reads2contigs.paf.gz Program starts [M::aa_pb] collecting positio...
purge_dups是用C语言编写,因此需要通过make来编译 git clone https://github.com/dfguan/purge_dups.git cd purge_dups/src && mak 脚本在scripts目录下,编译的程序在bin目录下 软件运行 输入文件分为两种,一种是组装序列,一种是测序数据。其中组装序列分为两种情况考虑,一种是类似falcon-unzip输出的primary asse...
Hi, I have a ~20Gb primary hifiasm genome, and it takes ~5 days for mapping one cell HiFi reads (~2000000 reads, 35Gb) to the genome (command: minimap2 -xasm20 -I -t6 asm.bp.p_ctg.fa hifi_reads.fa.gz |gzip -c - >cell1.paf.gz). And now th...
Hello, I'm running the first step of your pipeline guideline with ONT data, my only modification is -ax map-ont when calling minimpa2. The paf.gz is created correctly, however I see that pbcstat *.paf.gz gives a PB.stat file with only ze...