NicMAlexandre

Thank you! On Wed, Jun 16, 2021 at 10:00 AM chhylp123 ***@***.***> wrote: > > 1. Yes. > 2. Either is fine. With or without Hi-C share same bin files....

Two questions: 1. Do hifi reads need to be filtered for quality before inputting to Hifiasm? 2. Do I need to deduplicate or adapter trim Hifi reads? On Wed, Jun...

Thank you! On Mon, Aug 30, 2021 at 7:16 PM chhylp123 ***@***.***> wrote: > I guess it should be better to do QC first. You can directly use PB >...

I’m a little confused because when we run with -I0, there is a p_ctg and an a_ctg output. So if those alternate contigs are in p_ctg, then what is in...

Right, but when we run hifiasm with -l0, we have a non-empty a_ctg.fa file and a p_ctg.fa file. So I'm not understanding how anything could be in the a_ctg file...

I see I see that makes total sense now!! Nicolas On Fri, Oct 1, 2021 at 5:47 PM chhylp123 ***@***.***> wrote: > I guess real samples cannot be fully homozygous?...

We also tried the following with the same result: psmc/utils/./splitfa genome.fasta 35 | split -l 20000000 #mappability_kmers.list contains the following xaa xab xac for x in $(cat mappability_kmers.list); do bwa...

Hi Jeb, I reached out to Robert Hubley via email and sent him the relevant files and he said he would get back to me. I will let you know...

The goal is to print the insertion as the call in the consensus in this case. I should note that the reference is a different species, so there are expected...

Here is the head of the XML file ``` MNLDRLRKRVRHYIDQQQYQSALFWADKVSSLSHEDPQDIYWLAQCLYLTAQYHRASHALRSRKLDKLYGACQYLAARCHYAAKEYQQALDILDMEEAASKRLLDKNVKEDNGSRETVKEWEMSPASINSSICLLRGKIYDAMDNRPLATSSYKEALKLDVYCFEAFDLLTSHHMLTAQEEKDFLDSLPLSQQCTEEEVELLRFLFENKLKKYNKPSEMVVPDIVNGLQDNLDVVVSLAERHYYNCDFKMCYSLTSMVMVKDPFHANCLPVHIGTLVELSKANELFYLSHKLVDLYPSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLERTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNPKLAERFFSQALSIAPEDPFVIHEVAVVAFQNGDYKTAEKLFLDAMDKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYDQALEYHRQALVLIPQNASTYSAIGYVHSLMGDFESAIDYFHTALGLKRDDTFSVTMLGHCIEMYISDSDAYIGTDIKDKVRKTLGTPALMKMLNTSTEANESRAQPVEEVNVCLETPSFNADKQTDAFQRFLLECDMHENDMMLETSMSDTST ```