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28 Open 19 Closed
28 Open 19 Closed
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Issues list

Option to preserve MM/ML tags
#48 opened Sep 5, 2024 by aliceedoe
1
Sequence information not present in BAM file when mapping quality is 0 for a read
#47 opened Aug 30, 2024 by jagadhesh89
1
ERROR: input list of k-mers and winnowmap parameter k are inconsistent
#46 opened Jul 18, 2024 by zhyx6511
5
Seeing multiple primary alignments per read
#44 opened Feb 21, 2024 by mwykes
Detect deletion between gene and pseudogenes
#42 opened Nov 7, 2023 by keenhl
Is there any relevant evaluation for winnowmap2 with RNA-Seq data (like ont, iso-seq)?
#41 opened Nov 1, 2023 by shengxinzhuan
1
No -I option
#40 opened Aug 19, 2023 by soisa001
7
Mutilple references
#37 opened Feb 2, 2023 by Meghuser
2
Optimising gaps in whole genome assembly alignments
#34 opened Aug 17, 2022 by mnshgl0110
2
Try to understand the super long soft/hard clipping in the raw reads mapping
#33 opened Aug 14, 2022 by WenyuLiang
How to map with pre-built indexes ?
#32 opened Apr 14, 2022 by AbhinavDutta
2
Not compiling on MacOS ARM
#31 opened Mar 14, 2022 by jianshu93
2
Hard coded OMP threads?
#30 opened Feb 24, 2022 by johannesgeibel
2
failed to parse the FASTA/FASTQ record
#27 opened Sep 7, 2021 by Gongjiao94
3
PacBio CLR reads
#26 opened Sep 5, 2021 by OliverPStuart
1
How to change the mapQ and τ？
#25 opened Aug 20, 2021 by wangzhennan14
1
aligning HiFi reads to single pass long reads
#23 opened Aug 9, 2021 by dcopetti
2
[trivial] releases seem to be tar's, not tar.gz's
#22 opened Jul 20, 2021 by SHuang-Broad
1
Way to filter winnowmap2 BAM files for read lengths
#20 opened Jul 2, 2021 by Musketeer-D
Finding X scaffolds in a genome assembly
#19 opened Jun 22, 2021 by desmodus1984
Multithreading support?
#18 opened Jun 2, 2021 by zhemingfan
2
Winnowmap for read overlapping
#17 opened Jun 1, 2021 by shelkmike
3
Is --split-prefix supported?
#16 opened Apr 4, 2021 by schorlton
2
Much more unmapped reads compared to minimap2
#10 opened Dec 24, 2020 by yipukangda
List of files / multiple files as input
#9 opened Nov 22, 2020 by SergejN
5
ProTip! Exclude everything labeled bug with -label:bug.