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lentendu
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DeltaMP
A flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
GNU General Public License v3.0
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Silence pip 2.7 deprecation warning
#136
lentendu
closed
3 years ago
0
Update ebi api html addresses for automatic reads and metadata files download
#135
lentendu
closed
1 year ago
0
Enforce minimum length for ASV
#134
lentendu
closed
3 years ago
0
Add options to control the increment of length and maxee optimization
#133
lentendu
closed
3 years ago
1
Wrong sample order in count_table for large number of sample
#132
lentendu
closed
3 years ago
0
Decompression on symlink only works with -ck options
#131
lentendu
closed
3 years ago
0
Avoid any stat on primer removal when Remove primers at reads ends set to no
#130
lentendu
closed
3 years ago
0
Allow partial matches for open-reference clustering
#129
lentendu
closed
3 years ago
1
Use discriminant directory names for demultiplexing multiple libraries
#128
lentendu
closed
4 years ago
0
List files of array job only for the last task
#127
lentendu
closed
3 years ago
1
Control anchoring for demultiplexing and primer clipping
#126
lentendu
closed
4 years ago
0
Correct read count table and avoid R replacing dash by period in sample names
#125
lentendu
closed
4 years ago
0
Avoid excess use of memory by dada2 at OTU step
#124
lentendu
closed
4 years ago
1
Cap maximum truncation length
#123
lentendu
closed
4 years ago
0
Skip minimum read counts threshold for some samples
#122
lentendu
closed
4 years ago
0
Disable clustering reduction of same taxa reference sequences in cutdb
#121
lentendu
closed
4 years ago
0
Automatically detect original run library names in sequence filenames to execute dada2 per run without the need for demultiplexing
#120
lentendu
closed
4 years ago
1
Use cut reference database as prior knowledge to dada2 error correction algorithm
#119
lentendu
opened
4 years ago
0
substitute column by underscore in sequence identifier for vsearch trimmed Illumina reads
#118
lentendu
closed
4 years ago
0
Checkpointing failed when starting at a step with array hold
#117
lentendu
opened
4 years ago
0
For sequencing with primers not linked to R1/R2 libraries, keep both flavors separated for the optimization
#116
lentendu
closed
4 years ago
0
Reflect MOTHUR allowance of "-" in file names starting from v1.44.0
#115
lentendu
closed
4 years ago
0
Illumina demultiplexing with tag only associated to forward or reverse primer
#114
lentendu
closed
4 years ago
0
Allow thresholding read counts on ratio of raw reads, not only fixed counts
#113
lentendu
closed
4 years ago
1
Match raw_archiver dynamic names in steps.summary and ref.steps and avoid re-archiving of raw reads
#112
lentendu
closed
4 years ago
0
Improve job error detection
#111
lentendu
closed
4 years ago
0
Parallelize demultiplexing
#110
lentendu
closed
4 years ago
0
Demultiplex dual-indexing
#109
lentendu
closed
4 years ago
1
Download EBI SRA raw reads using the Aspera client
#108
lentendu
closed
4 years ago
0
Allow single Illumina library
#107
lentendu
opened
4 years ago
0
Allow linked primers for 454, and disable length optimization
#106
lentendu
opened
4 years ago
0
Filter protists OTUs
#105
lentendu
closed
4 years ago
0
Output swarm internal structure
#104
lentendu
closed
4 years ago
0
Set module name and modulefiles directory
#103
lentendu
closed
4 years ago
0
Include array holding in checkpointing resolution
#102
lentendu
closed
4 years ago
0
Both direction demultiplexing for 454
#101
lentendu
opened
4 years ago
0
Delete intermediary files in all steps
#100
lentendu
closed
4 years ago
0
Cap the number of cpu requested for get step
#99
lentendu
closed
4 years ago
1
Array job dependencies with corresponding task ID
#98
lentendu
closed
4 years ago
0
Symlink all targets to be archive in archive output and processing directories
#97
lentendu
closed
4 years ago
0
Add expected errors to raw and pair-end quality informations
#96
lentendu
opened
4 years ago
0
Re-format the grouping and clustering information
#95
lentendu
closed
4 years ago
1
bz2 compress sequence files at the end of each step
#94
lentendu
closed
4 years ago
1
Reduce time and memory footprint
#93
lentendu
closed
4 years ago
0
Parallelize get step
#92
lentendu
closed
4 years ago
0
Implement DADA2 ASV calling
#91
lentendu
closed
4 years ago
2
Update SRA ftp URLs for test libraries
#90
lentendu
closed
5 years ago
0
Implement pair-end merge with VSEARCH
#89
lentendu
closed
4 years ago
0
LAST_REF_JOBID not assign when checkpointing
#88
lentendu
opened
5 years ago
1
Add missing informations on cutadapt usages for primer removal in make_doc
#87
lentendu
opened
5 years ago
1
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