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…
# 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...
purge_dups软件的工作流程如上图分为三部分:1.首先将用于组装的三代测序数据比对到primary-assembly以计算基因组各部分覆盖度;2.primary-assembly自身的比对;3.将前两部分信息整合来推断出primary-assembly里的haplotigs和overlaps. 软件安装 purge_dups软件主页:https://github.com/dfguan/purge_dups ## purge_dups...
Purge_Dups purge haplotigs and overlaps in an assembly based on read depth Directory Structure scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py. scripts/run_purge_dups.py: script to run the purge_dups pipeline. ...
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 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 ...
~/opt/biosoft/purge_dups/bin/get_seqs dups.bed $asm 这里的purged.fa就是最终结果,junk, haplotig和duplication都会在hap.fa中。 可选步骤: 将alternative assembly和输出度hap.fa进行合并,然后运行上面四步,得到的purge.fa就是新的alternative assembly,而输出的hap.fa则是junk或overrepresented序列。
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...
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...