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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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Feature: allow to re-use same optimize quality parameters than a previous subproject
#186
lentendu
closed
11 months ago
0
Force all samples to belong to the same run for ASV error modl building
#185
lentendu
closed
1 year ago
0
Set a minimum amount of raw reads found in one orientation to consider this orientation
#184
lentendu
closed
1 year ago
0
Accept gz compress database fasta files
#183
lentendu
opened
1 year ago
0
Force analyses for unpairable datasets
#182
lentendu
closed
1 year ago
0
Cluster with multiple previous sub-projects
#181
lentendu
closed
1 year ago
0
Add version and commit number in env for backward compatibility
#180
lentendu
closed
1 year ago
0
Issue with ASV and swarm clustering not accepting N's
#179
lentendu
opened
1 year ago
0
Change minimum number of rank depending on database for cut_db
#178
lentendu
closed
1 year ago
0
More systematic compression at all levels
#177
lentendu
closed
1 year ago
0
Feature: provide manually curated reference sequences to use for taxonomic identification
#176
lentendu
closed
4 months ago
0
Feature: similarity based clustering for pair-end sequences which cannot be assembled
#175
lentendu
opened
1 year ago
0
Problem with cutadapt and anchored adapters
#174
lentendu
closed
1 year ago
0
Problem with restart from step when cut_db in the steps
#173
lentendu
opened
1 year ago
0
Allow disabling DADA2 bimera removal
#172
lentendu
closed
1 year ago
1
Add NGmerge as alternative pair-end algorithm
#171
lentendu
closed
1 year ago
0
Add header option to mimato
#170
lentendu
closed
1 year ago
0
Allow different set of parameters for checkpointing
#169
lentendu
closed
1 year ago
0
Avoid error if all reads already used in one direction for bidirectionnal libraries
#168
lentendu
closed
1 year ago
0
Adapt raw stat R scripts to R 4
#167
lentendu
closed
1 year ago
0
Simplify demultiplexing Illumina as cutadapt now supports parallel computation for demultiplexing
#166
lentendu
closed
1 year ago
0
Add configuration parameter to assign standard and large memory node to different partition names
#165
lentendu
closed
1 year ago
0
Replace OBITools and MOTHUR by seqkit and vsearch where possible
#164
lentendu
opened
1 year ago
0
Allow for possibility to truncate only based on expected error
#163
lentendu
closed
1 year ago
1
Add average expected truncation parameter to force optimization to reads of expected length
#162
lentendu
closed
1 year ago
0
Declare COMP and DECOMP in deltamp main
#161
lentendu
closed
1 year ago
0
Illumina_demulti find in late array job drop errors for missing files removed by other arrays
#160
lentendu
closed
1 year ago
1
Check for missing samples at demultiplexing
#159
lentendu
closed
1 year ago
0
Avoid any array script to fail when no more reads in the sample
#158
lentendu
closed
1 year ago
0
Correct Phred score optimized quality value selection for no truncation
#157
lentendu
closed
1 year ago
0
Update correct behaviour for TRUNCLEN
#156
lentendu
closed
2 years ago
0
Fix some Readme and configuration parameter misspelling
#155
lentendu
closed
2 years ago
0
Checkpointing with only a new database should start at id step
#154
lentendu
closed
2 years ago
1
Avoid dada2 R scipts to failed when no reads after pair-end merge
#153
lentendu
closed
1 year ago
0
Avoid stat_figure R scripts of Illumina_quality step to fail for empty files
#152
lentendu
closed
2 years ago
0
Read counts for truncated reads not in the same order than raw reads counts
#151
lentendu
closed
1 year ago
0
Add a Maximum length truncation for unpaired reads
#150
lentendu
closed
2 years ago
0
Use find for demultiplexing to avoid "too many arguments" error
#149
lentendu
closed
2 years ago
0
Remove all conversion of number of mismatch to proportion
#148
lentendu
opened
2 years ago
0
Allow more targets and database origins
#147
lentendu
closed
2 years ago
0
Use number of mismatches allowed on the primer sequences from the configuration file to cut database
#146
lentendu
closed
2 years ago
0
Avoid primer removed and pair-end fastq in raw demultiplex reads archiving for Illumina
#145
lentendu
closed
4 months ago
0
Disable old fashion two step assignment for ITS sequences
#144
lentendu
closed
2 years ago
0
Allow N's in barcodes for Illumina demultiplexing
#143
lentendu
closed
3 years ago
0
Rename asv representative sequences with sha1
#142
lentendu
closed
3 years ago
0
Add asv step between trim and OTU for better parallelization whith multiple libraries and pool approach
#141
lentendu
closed
3 years ago
0
When integrating back OTUs at end of id step, control for samples removed from count_table
#140
lentendu
closed
3 years ago
0
Include the repseq in cons taxonomy files to ensure correct link between taxonomy and count data
#139
lentendu
closed
3 years ago
0
Replace OTU by ASV wherever needed
#138
lentendu
closed
3 years ago
0
Handle configuration file with barcodes when already demultiplexed
#137
lentendu
opened
3 years ago
0
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