tanger

Can't Bio.pairwise2 align two very long sequences(50kbp and 100kbp)?

7

Hi. I am aligning two long sequence(seq1 is 5wbp, seq2 is 10wbp) using Bio.pairwise2, but there is an error: `Process finished with exit code -1073741819 (0xC0000005)` Can't Bio.pairwise2 align such...

Hi. I'm genotyping SVs in the HG002 sample. The command I used is ``` for i in {1..22} do $graphtyper genotype_sv $ref_file_folder/GCA_chr${i}.fa $vcf_folder/chr${i}_sv/chr${i}.vcf.gz --sam=$bam_file_folder/chr${i}_surject_chr_sort.bam --region=chr${i} --output="graphtyper_chr${i}" & done wait ```...

How can I autoindex the HPRC graph using '--workflow map' correctly?

2

Hi. I have tried some ways to autoindex the HPRC graph, but I can't index it correctly. When I use the command `vg autoindex --workflow map -g chr21.gfa -T tmp`,...

When I use `vg call -T` to get the gaf file of each **snarl's traversals path**, I find that it does not contain **all combinations**. Does the file contain only...

Doesn't GraphAligner support `.vg` graph?

5

When I use `.vg` graph in GraphAligner's mapping command `GraphAligner -g chr21.vg -f chr21.fq -t 88 -a graphaligner_aln.gam -x vg,` there is something error:  Why did I get this...

Can VG simulate the third-generations long reads?

5

Hi. Now I have the `.gbz` graph file, and I want to simulate the third-generations `long reads` data from a pangenome graph. Can VG simulate the third-generations long reads? Or...

some questions in the paper.

2

Hi, I'm looking at your paper, but there are some questions I don't understand. In the `step 5`, Svtig2 is aligned to the `s6 and s7` nodes, but why is...