结果文件 purged.fa:去冗余后的基因组结果 dups.bed: 第一列为序列ID,即将被删除,如果序列中含N,则会被拆成ID_1、ID_1、ID_3等多挑contig 第二列第三列为其实终止位置,第四列为类型,第五列为比对到的序列ID 3.参考 De novo组装#04 | 基因组去冗余(purge_dups) 使用Purge_dups去冗余序列 发布于 2024
Run the following commands to intall purge_dups (required):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:...
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 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...
冗余序列的产生和多种因素有关,如 CLR 的测序错误,基因组自身的杂合性和重复序列的影响等等,purge_dups软件能根据read深度分析组装中haplotigs和overlaps(purge_dups is designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.)另外有时候我们又担心会过度 purge,所以purg...
~/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 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...
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...
~/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。