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MikkelSchubert
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paleomix
Pipelines and tools for the processing of ancient and modern HTS data.
https://paleomix.readthedocs.io/en/stable/
MIT License
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Paleomix output reads folder no fastq reads
#56
xuefenfei712
opened
4 months ago
2
Duplicated reads error
#55
laneatmore
closed
4 months ago
3
BWA terminated by SIGKILL, PALEOMIX in BAM pipline
#54
Uriwolkow
closed
5 months ago
2
Receieved a NodeError while running the pipeline
#53
farahwar
opened
7 months ago
1
Error with trimming SE adapters from sample
#52
Uriwolkow
closed
7 months ago
2
Errors running node
#51
renhamm
closed
11 months ago
2
conda environment perpetually solving during installation
#50
renhamm
closed
1 year ago
6
BWA backtrack additional options added to samse, not aln
#49
DeondeJager
closed
1 year ago
3
Phylo pipeline "unknown command"
#48
974ben
closed
1 year ago
2
similar bams with rescale and non rescale
#47
fpezzini
closed
1 year ago
2
Issue When Employing `RegionsOfInterest`.
#46
g-pacheco
closed
1 year ago
6
Paleomix can not find picard even though it is there
#45
themudo
closed
2 years ago
8
biobambam2 instead of picard-tools?
#44
sameoldmike
opened
2 years ago
10
Should the .rmdup.collapsed.bam and .rmdup.normal.bam be merged?
#43
vitalirazumov
closed
1 year ago
1
A problem of PALEOMIX 2.0.0-alpha documentation
#42
YoungLU1
closed
2 years ago
2
BOWTIE2 errors in the pipeline
#41
ArchaeologyRoz
closed
2 years ago
8
About the MinQuality setting
#40
ztang040
closed
1 year ago
6
checkpointing
#39
kimh11
closed
3 years ago
2
ImportError: libhts.so.2: cannot open shared object file: No such file or directory
#38
sagitaninta
closed
3 years ago
14
paleomix bam_pipeline: error: unrecognized arguments: --gatk_max_threads=1 --progress_ui=running --jre_options=
#37
Rhinogradentia
closed
3 years ago
5
"Could not retrieve index file"
#36
ab08028
closed
3 years ago
1
readthedocs Documentation incorrectly renders double dash with a 'long' single dash
#35
jfy133
closed
3 years ago
0
thank you, but this message appears with PALEOMIX v.1.2.14 too
#34
flaviode
closed
3 years ago
3
Java issue with an updated openjdk version
#33
flaviode
closed
4 years ago
1
Add conda instructions to documentation
#32
jfy133
closed
4 years ago
1
[info] conda instructions for paleomix
#31
jfy133
closed
4 years ago
1
Error running mapDamage in example bam_pipeline
#30
Rhinogradentia
closed
4 years ago
2
Alignment to sequence variation graph?
#29
nwales
opened
4 years ago
1
Paleomix expecting gatk.jar to be in a specific folder?
#28
gtrichard
closed
4 years ago
3
pip install seems broken
#27
gtrichard
closed
4 years ago
4
GATK error
#26
deFerran
closed
4 years ago
2
"Positional data is too large for BAM format"
#25
lindenb
closed
4 years ago
4
paleomix doesnot work
#24
xuefenfei712
closed
3 years ago
8
GATKv4 not supported?
#23
mscbig
closed
4 years ago
2
bam_pipeline error
#22
denise0593
closed
4 years ago
2
Paleomix bam_pipeline error
#21
nsmt89
closed
5 years ago
1
Phylo pipeline example not working
#20
teepean
closed
4 years ago
1
Issue running the example bam_pipeline
#19
ldutoit
closed
4 years ago
2
Trimming first 6-8 bp of read 1
#18
nwales
opened
5 years ago
2
documentation for paloemix phylo pipeline
#17
siriusb-nox
opened
5 years ago
1
write-config
#16
blondie5125
closed
5 years ago
2
Please switch to Python3
#15
tillea
closed
1 year ago
22
Tox tests do not work
#14
tillea
closed
6 years ago
0
Failure in build time test
#13
tillea
closed
6 years ago
1
Make vcf_to_fasta.py work with VCFs containing haploid genotype calls.
#12
grahamgower
closed
6 years ago
1
Please try to drop code copy of pyyaml
#11
tillea
closed
4 years ago
8
Soft clipped reads are not correctly deduplicated
#10
grahamgower
closed
7 years ago
6
time elapsed reset by using function keys
#9
ginolhac
closed
7 years ago
2
Update setup.py
#8
MikkelSchubert
closed
7 years ago
0
skip adapter-trimming
#7
ginolhac
closed
8 years ago
2
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