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Question: Best practice for aligning reads against two highly similar genomes

#51

· jacgonisa opened

on Mar 3, 2025

Winnowmap doesn't throw a [Warning] or [Error] when -W is empty

#50

· Isoris opened

on Jan 31, 2025

Option to preserve MM/ML tags

#48

· aliceedoe opened

on Sep 5, 2024

Sequence information not present in BAM file when mapping quality is 0 for a read

#47

· jagadhesh89 opened

on Aug 30, 2024

ERROR: input list of k-mers and winnowmap parameter k are inconsistent

#46

· zhyx6511 opened

on Jul 18, 2024

Seeing multiple primary alignments per read

#44

· mwykes opened

on Feb 21, 2024

Detect deletion between gene and pseudogenes

#42

· keenhl opened

on Nov 7, 2023

Is there any relevant evaluation for winnowmap2 with RNA-Seq data (like ont, iso-seq)?

#41

· shengxinzhuan opened

on Nov 1, 2023

No -I option

#40

· soisa001 opened

on Aug 19, 2023

Mutilple references

#37

· Meghuser opened

on Feb 2, 2023

Optimising gaps in whole genome assembly alignments

#34

· mnshgl0110 opened

on Aug 17, 2022

Try to understand the super long soft/hard clipping in the raw reads mapping

#33

· WenyuLiang opened

on Aug 14, 2022

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