OpenGene gencore issues

OpenGene / gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

MIT License

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issues

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unordered output will still appear in version 0.17.2

#54 xiechangxiao opened 5 months ago
0
Why gencore cannot treat single-end UMI read?

#53 polymerase2010 opened 9 months ago
0
genecore will change the MD:Z value in the bam after umi cluster？

#52 litun-fkby opened 11 months ago
0
fix#46 fix bug for Group::makeConsensus

#51 biolxy closed 1 year ago
1
gencore-0.17.2 incompatible with python 3.10, python 3.8, python 3.6 or python 2.7

#50 Wangxin555 opened 1 year ago
0
change 'nan' in output to 'NaN'

#49 TomaszSuchan opened 1 year ago
0
in overlap position, gencore doesn't reset quality

#48 wyy1234-github opened 1 year ago
0
gencore seems to have wrongly modified my SAM alignment record

#47 jammywwh opened 1 year ago
0
'=' symbol in the BAM/CRAM SEQ field

#46 ShannonDaddy closed 1 year ago
3
Reads with identical UMIs and mapping coordinates output by Gencore

#45 luederm opened 2 years ago
0
There are one or three reads with the same name after deduplication

#44 bio-Tao opened 2 years ago
0
SAM file validation errors after running gencore

#43 luederm opened 2 years ago
0
Mismatched UMI of a pair of reads

#42 litun-fkby opened 2 years ago
1
ERROR: Wrong base with value 0

#41 RainyEricYe opened 2 years ago
0
The software installation is not working properly.

#40 ChaoXianSen closed 2 years ago
1
what is the max number of interval in a bed for QC report

#39 xmzhuo opened 3 years ago
0
Prebuild versions of gencore in opengene.org with version history

#38 lavauxt opened 3 years ago
0
output bam without FR or RR tag

#37 Frank1219 closed 3 years ago
16
gencore don't generate consensus read from two pair reads with reciprocal UMI ,such as UMI ATGC_GCAA and GCAA_ATGC

#36 litun-fkby opened 3 years ago
1
Extracting UMIs for paired-end data

#35 Biojenifer closed 3 years ago
0
EOF markers absent

#34 pdimens opened 3 years ago
0
Gencore failed to process BAM generated by STAR aligner

#33 k1197445 opened 3 years ago
1
Data used in the paper?

#32 cagaser opened 3 years ago
0
write read groups

#31 antonkulaga opened 3 years ago
0
running speed very slow for me

#30 bhinderb opened 3 years ago
0
Add option to never toss reads

#29 FlorianErger opened 4 years ago
0
Insertion/deletion may cause UMI-based collapsing failed

#28 gudeqing closed 4 years ago
0
incorrect bam record sort function which might lead to core dump incidently

#27 wulj2 closed 4 years ago
0
bam records comperator fixed to satisfy the strick weak orderings, th…

#26 wulj2 closed 4 years ago
0
output read cluster information

#25 gudeqing opened 4 years ago
0
SV calling

#24 tyyiyi opened 4 years ago
0
Collapsing fails

#23 tahuh opened 4 years ago
0
Feature request: support deduplication based on [contig]:[R1 coordinate] only

#22 ijhoskins opened 4 years ago
3
Segmentation fault (core dumped) after loading contigs from BAM file

#21 vmkalbskopf opened 4 years ago
0
Mismatched UMI of a pair of reads

#20 Gerde closed 4 years ago
1
Nanopore or Pacbio HiFi data

#19 kokyriakidis opened 4 years ago
0
report error or?

#18 gatozee closed 4 years ago
1
Is it intended action? The read2 flag was converted to read1 flag.

#17 roh329 opened 4 years ago
2
output bam problem

#16 xin8you opened 4 years ago
6
No coverage at the end of the reference after using Gencore

#15 stefjanson opened 4 years ago
0
Testing gencore with a dummy fastq results in no clusters

#14 ChadFibke opened 4 years ago
0
Settings for liquid biopsy?

#13 kokyriakidis opened 4 years ago
2
请教个问题

#12 Liripo closed 4 years ago
1
合并umi问题

#11 zhujiaqi2014 closed 5 years ago
1
Behavior relative to picard?

#10 caleblareau opened 5 years ago
1
Single-end read with UMI

#9 caleblareau opened 5 years ago
3
UMI in Sam Tag

#8 caleblareau opened 5 years ago
2
running speed is too slow, only using one CPU

#7 billzt opened 5 years ago
6
Are Unmapped reads in the BAM file corrected ? or discarded ?

#6 chadisaad opened 5 years ago
0
typo

#5 smoretti opened 5 years ago
1