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poreCov
SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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Include artic-tools "validate_scheme"
#222
DataSpott
opened
2 years ago
1
added bar plot for LCS
#221
MarieLataretu
closed
2 years ago
3
Pangolin v4.0
#220
hoelzer
closed
2 years ago
11
MN908947.3 vs. NC_045512.2
#219
MarieLataretu
opened
2 years ago
0
Possible filtering issue
#218
tb-fyr
closed
1 year ago
5
Report also VCF files
#217
hoelzer
closed
1 year ago
11
init LCS pooled sample implementation
#216
replikation
closed
2 years ago
1
SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly
#215
thomasbtf
closed
1 year ago
0
adding new db
#214
replikation
closed
2 years ago
1
Table style updates
#213
RaverJay
closed
2 years ago
9
V2 -> V2a, pool fix, consistent ordering
#212
bwlang
closed
2 years ago
3
Custom bed
#211
replikation
closed
2 years ago
2
Variant calling doesn't seem to work with VarSkipV2
#210
JaMaack
closed
2 years ago
3
Updated Midnight primer kit
#209
hoelzer
closed
2 years ago
4
seqrs V4.1 support and singularity envWhitelist
#208
MarieLataretu
closed
2 years ago
1
improve table style
#207
replikation
closed
2 years ago
12
Report VOCs, VOIs etc
#206
RaverJay
closed
2 years ago
10
add frameshift column
#205
RaverJay
closed
2 years ago
0
update guppy
#204
replikation
opened
2 years ago
4
adding VarSkip2 primer
#203
replikation
closed
2 years ago
2
ARTIC V4.1 official primers
#202
hoelzer
closed
1 year ago
0
Integration of VarSkip NEB primern
#201
BoehmONT
closed
2 years ago
21
read_classification_wf:kraken2 fails on Mac
#200
CSynodinos
closed
2 years ago
9
Frameshift detection
#199
hoelzer
closed
2 years ago
4
Use nextclade aa insertions
#198
RaverJay
closed
2 years ago
6
Report commandline
#197
RaverJay
closed
2 years ago
2
bump Medaka version in ARTIC container
#196
hoelzer
closed
2 years ago
2
Nanopolish mode: report requests
#195
hoelzer
closed
2 years ago
5
Run --nanopolish on already basecalled data
#194
hoelzer
closed
2 years ago
1
File name collision due to "." in the file name
#193
hoelzer
closed
2 years ago
5
Catch identical filenames
#192
MarieLataretu
opened
2 years ago
5
Improve Documentation
#191
oliverdrechsel
closed
1 year ago
5
Report classification as VOI, VOC, ... of lineages in results table
#190
oliverdrechsel
closed
2 years ago
12
Implement stable reporting of AA insertions, possibly snpEff
#189
RaverJay
closed
2 years ago
5
Fix V4.1 primer file: replace spaces with tabs
#188
RaverJay
closed
2 years ago
0
Using consensus fasta type as PoreCov input
#187
bioinfo-ebiogen
closed
2 years ago
3
add ARTIC v4.1 spike in profile
#186
oliverdrechsel
closed
2 years ago
4
nextclade pos is now the nucleotide before the insertion
#185
RaverJay
closed
2 years ago
8
Omicron: report shows insertion S:A213AEPE although S:R214REPE is the (likely) correct one
#184
hoelzer
closed
2 years ago
7
Add mid strand barcode detection to guppy
#183
replikation
closed
2 years ago
3
added V4.1 fixes #175
#182
MarieLataretu
closed
2 years ago
5
--update does only update Pangolin or Nextclade ?
#181
hoelzer
closed
2 years ago
3
Guppy adjustments for HPC (SLURM) execution
#180
hoelzer
closed
2 years ago
0
Idea for the report table: A mini-plot that shows where Ns are in the assemblies
#179
RaverJay
opened
2 years ago
14
KrakenDB update
#178
oliverdrechsel
closed
1 year ago
3
add aa insertions from Nextclade
#177
RaverJay
closed
2 years ago
6
Add Scorpio + constellations column and versions
#176
RaverJay
closed
2 years ago
13
ARTIC V4.1 primer scheme for Omicron
#175
hoelzer
closed
2 years ago
9
Add parameter to publish more results
#174
hoelzer
closed
1 year ago
2
Add Scorpio
#173
hoelzer
closed
2 years ago
5
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