OpenGene / gencore

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

OpenGene/gencore Issues

gencore don't generate consensus read from two pair reads with reciprocal UMI ,such as UMI ATGC_GCAA and GCAA_ATGC
Updated 3 months ago1
Why gencore cannot treat single-end UMI read?
Updated 3 months ago
genecore will change the MD:Z value in the bam after umi cluster？
Updated 5 months ago
'=' symbol in the BAM/CRAM SEQ field
Closed 7 months ago3
gencore-0.17.2 incompatible with python 3.10, python 3.8, python 3.6 or python 2.7
Updated a year ago
change 'nan' in output to 'NaN'
Updated a year ago
in overlap position, gencore doesn't reset quality
Updated a year ago
gencore seems to have wrongly modified my SAM alignment record
Updated a year ago
Gencore failed to process BAM generated by STAR aligner
Updated 2 years ago1
Is it intended action? The read2 flag was converted to read1 flag.
Updated 2 years ago2
Mismatched UMI of a pair of reads
Updated 2 years ago1
Reads with identical UMIs and mapping coordinates output by Gencore
Updated 2 years ago
There are one or three reads with the same name after deduplication
Updated 2 years ago
SAM file validation errors after running gencore
Updated 2 years ago
ERROR: Wrong base with value 0
Updated 2 years ago
The software installation is not working properly.
Closed 2 years ago1
Feature request: support deduplication based on [contig]:[R1 coordinate] only
Updated 3 years ago3
what is the max number of interval in a bed for QC report
Updated 3 years ago
output bam without FR or RR tag
Closed 3 years ago16
Prebuild versions of gencore in opengene.org with version history
Updated 3 years ago
Extracting UMIs for paired-end data
Closed 3 years ago
EOF markers absent
Updated 3 years ago
Data used in the paper?
Updated 3 years ago
write read groups
Updated 3 years ago
running speed very slow for me
Updated 3 years ago
about single-read seqence
Updated 3 years ago1
Insertion/deletion may cause UMI-based collapsing failed
Closed 4 years ago
UMI in Sam Tag
Updated 4 years ago2
Add option to never toss reads
Updated 4 years ago
incorrect bam record sort function which might lead to core dump incidently
Closed 4 years ago
output read cluster information
Updated 4 years ago
SV calling
Updated 4 years ago
Collapsing fails
Updated 4 years ago
Mismatched UMI of a pair of reads
Closed 4 years ago1
Segmentation fault (core dumped) after loading contigs from BAM file
Updated 4 years ago
Nanopore or Pacbio HiFi data
Updated 4 years ago
report error or?
Closed 4 years ago1
running speed is too slow, only using one CPU
Updated 4 years ago6
output bam problem
Updated 4 years ago6
No coverage at the end of the reference after using Gencore
Updated 4 years ago
Testing gencore with a dummy fastq results in no clusters
Updated 4 years ago
Settings for liquid biopsy?
Updated 4 years ago2
how to set umi mismatch and umi cluster method?
Updated 4 years ago2
请教个问题
Closed 4 years ago1
Single-end read with UMI
Updated 5 years ago3
Behavior relative to picard?
Updated 5 years ago1
合并umi问题
Closed 5 years ago1
Are Unmapped reads in the BAM file corrected ? or discarded ?
Updated 5 years ago
typo
Updated 5 years ago1
How to set up the base quality of a concensus read?
Updated 5 years ago