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hariszaf
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pema
PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes
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Wrong sample names in OutputPerSample
#69
JustinePa
opened
3 months ago
5
Long recurrent taxonomic labels
#68
stas-malavin
closed
5 months ago
1
pandaseq error "Something is wrong with this ID"
#67
stas-malavin
closed
6 months ago
17
Update "PEMA's output files.md" (fixes #62)
#66
JustinePa
closed
8 months ago
1
Storage usage of PEMA
#65
savvas-paragkamian
opened
9 months ago
1
Changes in parameters file, READme, and output folders for v.2.1.5
#64
savvas-paragkamian
closed
9 months ago
0
time consuming preprocessing
#63
hariszaf
opened
9 months ago
0
Needed updates on "PEMA's output files.md"
#62
JustinePa
opened
10 months ago
2
When Swarm is chosen for the ITS, the names of the sequences are OtuXX and not ASVXX
#61
cpavloud
opened
11 months ago
4
16s copy number
#60
hariszaf
opened
11 months ago
0
Error PEMA ASV inference: Directory swarm does not exists
#59
savvas-paragkamian
closed
9 months ago
5
Unexpected Singletons in Final Table despite removeSingletons set to "Yes"
#58
JustinePa
closed
1 year ago
5
Arms
#57
hariszaf
closed
1 year ago
0
MIDORI updates
#56
kmexter
opened
1 year ago
2
PEMA to create a run summary file
#55
kmexter
opened
1 year ago
2
PEMA Ro-Crate
#54
kmexter
opened
1 year ago
1
extended final table
#53
kmexter
opened
1 year ago
1
provide pema main data product in a 7-level taxonomy format
#52
hariszaf
opened
1 year ago
3
Upgrade to crest4
#51
hariszaf
opened
1 year ago
0
custom_ref_db doesn't work.
#50
hyeiny119
closed
1 year ago
5
HPC job specifications
#49
marymcelroy
closed
1 year ago
4
Error when unzipping using a checkpoing
#48
hariszaf
closed
1 year ago
1
add remove_singletons option in OTU pipeline
#47
natgiot
closed
1 year ago
4
MAPseq alternative classifier for the case of rRNA genes
#44
hariszaf
opened
2 years ago
0
Option of running PEMA in distinct steps
#43
georgiatari
closed
1 year ago
2
PEAR as merging algorithm in PEMA
#42
georgiatari
closed
2 years ago
1
alternative database for COI marker gene
#41
hariszaf
closed
2 years ago
2
Enhancement: Add option for users to provide a custom adapter file
#40
natgiot
opened
2 years ago
1
Enhancement: Add bbmap suite for read preprocessing
#39
natgiot
opened
2 years ago
1
Describe formally the pema output
#38
hariszaf
opened
2 years ago
2
essential fixes to make the embeded yaml parse
#37
marc-portier
closed
2 years ago
3
Species level missed in `finalTable.tsv`
#36
hariszaf
closed
2 years ago
0
Parameters file in a structured format
#35
hariszaf
opened
2 years ago
12
ITS sanity check fails
#34
probonas
closed
2 years ago
1
Arms
#33
hariszaf
closed
2 years ago
0
Add 12S marker gene
#32
hariszaf
closed
2 years ago
3
PEMAbase needs to be indenpendent from any local files
#31
hariszaf
closed
2 years ago
4
NCBI Taxon ID included in the final_table.tsv file?
#29
cpavloud
opened
2 years ago
12
Data provenance considerations
#28
cpavloud
closed
2 years ago
6
Consider incorporating tools for pseudogene detection
#27
cpavloud
opened
2 years ago
3
Add new database for 16S/18S (SILVA 138)
#26
cpavloud
closed
2 years ago
1
Empty 8.outputPerSample folder
#25
cpavloud
closed
2 years ago
3
Fail with 18S data and swarm algorithm
#24
cpavloud
closed
2 years ago
1
Conversion to ENA format - Sample names
#23
cpavloud
closed
2 years ago
4
Fail with 18S data and vsearch algorithm
#22
hariszaf
closed
2 years ago
3
Add alternative db for the case of 18S rRNA
#21
hariszaf
closed
2 years ago
1
Add alternative ref db for the case of COI
#20
hariszaf
opened
2 years ago
1
Convert raw data from other than MiSeq sequencers to PEMA format
#19
hariszaf
closed
2 years ago
0
Develop
#14
hariszaf
closed
3 years ago
0
PEMA dependencies
#13
deniskristak
closed
2 years ago
4
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