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Zymo-Research
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aladdin-shotgun
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0.0.12
#117
zxl124
closed
6 hours ago
0
Sourmash database and default kmer update
#116
zxl124
closed
1 day ago
0
Composition bar plots in the report wouldn't display for large number of samples
#115
zxl124
opened
4 weeks ago
0
CITATIONS.md update
#114
nsharp2
closed
4 days ago
0
add check for empty samples or no samples after filtering
#113
zxl124
closed
2 months ago
0
Out of Memory Error in resistome_snpverify fixed
#112
nsharp2
closed
2 months ago
0
Out of Memory Error in resistome_snpverify fixed
#111
nsharp2
closed
2 months ago
1
Resistome SNPverify would run out of memory without retrying
#110
zxl124
opened
2 months ago
0
Empty samples after host match filtering (sourmash) crash the pipeline
#109
zxl124
closed
6 hours ago
1
0.0.11
#108
zxl124
closed
2 months ago
0
fastp would hang forever when one of PE FASTQ files are truncated
#107
zxl124
closed
2 months ago
0
FastQC exit with 0 status when one of PE reads are incorrect
#106
zxl124
closed
2 months ago
0
0.0.10
#105
zxl124
closed
3 months ago
0
remove --stdout from fastp commands
#104
zxl124
closed
3 months ago
0
fastp writing large amounts of data to STDOUT
#103
zxl124
closed
2 months ago
0
Updates for 0.0.9
#102
zxl124
closed
3 months ago
0
update sourmash threshold_bp to 5000
#101
zxl124
closed
3 months ago
0
sourmash default threshold_bp too long for viruses
#100
zxl124
closed
3 months ago
0
change s3 address for beta diversity files
#99
zxl124
closed
4 months ago
0
beta diversity deliverables not corrected delivered on Aladdin
#98
zxl124
closed
3 months ago
0
temporary fix for ARM++ SNP verify
#97
zxl124
closed
4 months ago
0
Temporary Bug Fix: AMR++ TypeError "string indices must be integer"
#96
nsharp2
closed
4 months ago
0
AMR++ SNPverify error
#95
zxl124
opened
4 months ago
1
0.0.7 changes
#94
zxl124
closed
4 months ago
0
make sourmash filtering optional; change lowread to 1k
#93
zxl124
closed
4 months ago
0
SNP verified AMR++ results now available on aladdin platform
#92
nsharp2
closed
4 months ago
0
Single end AMR++ analysis enabled
#91
nsharp2
closed
5 months ago
0
For samples with fewer reads, default sourmash parameters and filter parameters don't work
#90
zxl124
closed
3 months ago
0
sourmash gather now uses STDOUT instead of STDERR
#89
nsharp2
closed
5 months ago
0
sourmash gather log not properly collected.
#88
zxl124
closed
5 months ago
1
sourmash gather run out of memory at k=21 for some samples.
#87
zxl124
opened
5 months ago
0
When all samples fail lowread_filter, pipeline errors
#86
zxl124
opened
5 months ago
1
changes for 0.0.6
#85
zxl124
closed
5 months ago
0
summarize_downloads.py updated after amr normalization added
#84
nsharp2
closed
5 months ago
0
normalize amr script added to pipeline
#83
nsharp2
closed
5 months ago
0
AMR counts tables added to files_to_download.json
#82
nsharp2
closed
5 months ago
0
Merge wastewater code to dev
#81
zxl124
closed
6 months ago
0
merge AMR code to dev
#80
zxl124
closed
6 months ago
0
Addition of AMR plus plus modules
#79
nsharp2
closed
5 months ago
1
RESISTOME_SNPVERIFICATION updated; top 20 genes barchart added
#78
nsharp2
closed
6 months ago
0
Resistome class results barchart; resistome snpverify process added
#77
nsharp2
closed
6 months ago
0
resistome run and resistome results scripts from AMRplusplus added
#76
nsharp2
closed
6 months ago
0
Merging changes to main into dev for consistency
#75
nsharp2
closed
6 months ago
0
beta diversity description updated for correctness
#74
nsharp2
closed
7 months ago
0
beta diversity section description error
#73
zxl124
closed
7 months ago
0
0.0.5 changes
#72
zxl124
closed
8 months ago
0
report title tracks -name
#71
zxl124
closed
8 months ago
0
sourmash use assembly IDs as keys
#70
zxl124
closed
8 months ago
0
updates for 0.0.4
#69
zxl124
closed
8 months ago
0
rebranding to aladdin
#68
zxl124
closed
8 months ago
0
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