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maickrau / GraphAligner

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Alignment error #83

Open GeorgeBGM opened 1 year ago

GeorgeBGM commented 1 year ago

Hi, I tried to use GraphAligner(GraphAligner -g CPC.HPRC.Phase1.CHM13v2_Non-W.gfa -f /HJ.stLFR_CCS.maternal.fasta.gz -a aln.gam -x vg), But I got several errors message.Can you give me some suggestions.

image

maickrau commented 1 year ago

Hi, could you try compiling the most recent commit and trying with that, and if it still gives errors then share the graph and the reads

GeorgeBGM commented 1 year ago

Hi, I tried to align the assembled sequences to the recently released human pan-genome using the latest GraphAligner and still have the following error reported. Do you have some suggestions about this? My main purpose is to increase the polymorphism of the released pan-genome using my own assembled sequences, and I feel that GraphAligner can achieve this effect, so do you have any suggestions about this issue?

The command is as follows: GraphAligner --threads 20 -g CPC.Phase1.CHM13v2-full_Non-W.gfa -f HJ.stLFR_CCS.maternal.fasta.gz -a aln_new.gam -x vg

GraphAligner：https://github.com/maickrau/GraphAligner/files/10706255/GraphAligner.tar.gz CPC.Phase1.CHM13v2-full_Non-W.gfa：https://pog.fudan.edu.cn/cpc/files/CPC.Phase1.CHM13v2-full/CPC.Phase1.CHM13v2-full.gfa.gz HJ.stLFR_CCS.maternal.fasta.gz：https://ftp.cngb.org/pub/CNSA/data2/CNP0001199/CNS0260311/CNA0017726/HJ.stLFR_CCS.maternal.fasta.gz

The result is as follows:

image image

Do you have recommended parameters or software to align the assembled genome to the existing pangenome?

GeorgeBGM commented 1 year ago

Hi, do you have any suggestion about this question, if I want to compare multiple genomes of my own assembly to the HPRC pan-genome, should I combine these assembled genomes in one file or compare them to the HPRC pan-genome separately?

maickrau commented 1 year ago

Could you try with the most recent commit 7877294? There was a similar bug in some other datasets, it might have fixed this one as well.

About the comparison, for aligning the sequences to the graph it doesn't matter whether you align one at a time or all at the same time. For the comparisons it might depend on what you want to do with the alignments.