NanoRepeat
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WGLab
NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
For example, straglr can add annotation to an vcf output with pathogenic_min and then call whether it is full_mutation, pre_mutation or normal, e.g. chr21 43776443 . G . PASS SVTYPE=STR;END=43776479;REF=5;RL=36;RU=GGGGCGC;REPID=CSTB;VARID=CSTB;STR_STATUS=pre_mutation;STR_NORMAL_MAX=3;STR_PATHOLOGIC_MIN=30;RankScore=1:20;HGNCId=2482;InheritanceMode=AR;DisplayRU=CCCCGCCCCGCG;SourceDisplay=GeneReviews_Internet_2019-11-07;Source=GeneReviews;SourceId=NBK535148;Disease=EPM1...
I am currently working on comparing different STR software to see how well they make the calls using ONT's latest Q20+ data for HG002. https://labs.epi2me.io/giab-2023.05/ I am using HG002 T2T...
Thanks for developing NanoRepeat. From my own testing, it seems to be doing much better than straglr. However, I find that NanoRepeat doesn't support IUPAC nucleotides in repeat unit but...
Hi Fang, I have a few questions regarding the handling of loci with interruptions and complex motifs in NanoRepeat. I saw that NanoRepeat supports joint quantification of two adjacent STRs....
Hi there, beautiful tool, thanks for developing it. I have a question related to the ```NanoRepeat_output.tsv```: Sometimes I noticed that instead of reporting ```Read_Repeat_Size``` and ```Read_Allele_ID```, ```-1``` is reported. Back...
At this point, I'm unsure what the tool expects, or what is wrong. From the READme I gathered it was not really tolerant to impure STR regions, so I made...
