Comments (2)
SAMtoBAM
commented on May 30, 2024
Apologies,
I had no notification that there was an issue opened!
I have tested it with illumina data also and it appears to work fine
In fact I avoid all scaffolding like with RaGOO as this only add issues with the gaps introduced (filled with N's)
For me the best is to break all the scaffolds before alignment
In terms of the contig renaming, there is no need for contigs to have any particular naming system
The naming in the test samples is just due to how they were produced
Have you been able to get it working?
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SAMtoBAM
commented on May 30, 2024
@koushik1989
is this still an issue?
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Related Issues (20)
- How to understanding the inversion result? HOT 3
- SV call from multiple genomes comparison HOT 8
- multiple threads? HOT 7
- awk: cmd. line:1: fatal: division by zero attempted HOT 4
- Total duplications and inversions between the homologous chromosomes of an haplotype-phased genome assembly HOT 7
- syntax error near unexpected token `newline' HOT 6
- Return to 'multiple threads?' closed issue HOT 5
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- What does it mean 'imprecise' calls for the VCF HOT 2
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- problems in inversion
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