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NBISweden
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aMeta
Ancient microbiome snakemake workflow
MIT License
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15
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making aMeta less pathogen oriented
#123
LeandroRitter
closed
1 year ago
0
Error: duplicates in sam-header when running Bowtie2 on full NT
#122
LeandroRitter
closed
1 year ago
2
Deamination takes too much time for large samples
#121
ZoePochon
closed
9 months ago
1
MapDamage is only applied to pathogens
#120
ZoePochon
closed
1 year ago
1
A rule is using pathogen specific file for filtering which should not be the case.
#119
ZoePochon
closed
1 year ago
1
Add conda lock file
#118
percyfal
closed
1 year ago
2
Fix error inserted in Samtools Faidx
#117
ZoePochon
closed
1 year ago
0
No rebuilding of bowtie2 database, Readme database download info, log file path correction fixing issue #85, no "number" in PMDtools
#116
ZoePochon
closed
1 year ago
0
added overview heatmaps and Main Results section to README
#115
LeandroRitter
closed
1 year ago
0
added authentication heatmap overview
#114
LeandroRitter
closed
1 year ago
0
added authentication score overview heatmap
#113
LeandroRitter
closed
1 year ago
0
WIP: Protect index
#112
percyfal
opened
1 year ago
2
Option to choose between filtering by TaxReads or Reads
#111
ZoePochon
closed
1 year ago
2
added heatmap summarizing krakenuniq abundance
#110
LeandroRitter
closed
1 year ago
0
fixed a bug in malt_abundance_matrix.R
#109
LeandroRitter
closed
1 year ago
0
RScript fails with one sample
#108
cb-scott
closed
1 year ago
1
added small fixes to damage.smk and krakenuniq_abundance_matrix.R
#107
LeandroRitter
closed
1 year ago
0
added more info to README, added small fix to authentic.R and more threads to fastqc
#106
LeandroRitter
closed
1 year ago
0
skip adapter removal step
#105
LeandroRitter
closed
9 months ago
3
mapdamage rule fails when no pathogen present
#104
LeandroRitter
closed
1 year ago
1
added more info to README and a small fix to authentic.R
#103
LeandroRitter
closed
1 year ago
0
added update Krona taxonomy instructions to README
#102
LeandroRitter
closed
1 year ago
0
added updating Krona taxonomy instruction to README
#101
LeandroRitter
closed
1 year ago
0
added --use-conda to docs
#100
LeandroRitter
closed
1 year ago
0
Modified README and added logo
#99
LeandroRitter
closed
1 year ago
0
Options or instructions for users with PE sequencing data
#98
LeandroRitter
closed
9 months ago
1
add brackets + true before the pmdtools pipe
#97
ZoePochon
closed
1 year ago
0
no full pathogen list pathogensFound.very_inclusive.tab is provided in aMeta repo
#96
LeandroRitter
closed
1 year ago
3
create_outdir
#95
ZoePochon
closed
1 year ago
0
create_outdir
#94
ZoePochon
closed
1 year ago
0
Fixes last part of issue #91
#93
ZoePochon
closed
1 year ago
2
extract taxid with regex
#92
clami66
closed
1 year ago
0
Malt_quantify_abundance rule broken
#91
ZoePochon
closed
1 year ago
1
Add support for multiple adapters
#90
percyfal
closed
1 year ago
4
export filtering step to standalone script
#89
clami66
closed
1 year ago
4
filter_krakenuniq, krakenuniq2krona, krakenuniq_abundance_matrix scripts overlap
#88
clami66
closed
1 year ago
2
Lower memory usage in kraken2krona
#87
clami66
closed
1 year ago
0
Impossible to give more threads to the rule "KrakenUniq2Krona"
#86
ZoePochon
closed
1 year ago
1
Warning regarding path for log file
#85
ZoePochon
closed
1 year ago
3
Pathogen-only projects
#84
ZoePochon
closed
1 year ago
7
Remove trailing sam files
#83
percyfal
closed
11 months ago
1
Simplify authentication output folders, filenames
#82
clami66
closed
1 year ago
0
revert to python3 for pmdtools
#81
clami66
closed
1 year ago
1
Add samtools faidx sequence retrieval
#80
percyfal
closed
1 year ago
2
Reduce get_ref_id verbosity
#79
percyfal
closed
1 year ago
0
add authentication score rule
#78
LeandroRitter
closed
1 year ago
0
add authentication score rule
#77
LeandroRitter
closed
1 year ago
1
add nextera adapter removal
#76
LeandroRitter
closed
1 year ago
0
cannot extract refid
#75
LeandroRitter
closed
1 year ago
3
krakenuniq-build v.0.7.3 cannot find jellyfish
#74
LeandroRitter
closed
1 year ago
2
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