Comments (3)
In GitLab by @lentendu on Feb 7, 2018, 16:02
- configuration parameter "ITSx region to extract"
- set variable "ITSX"
- variable possible values: no (default) / ITS1 / ITS2 (values for the ITSx option --save_regions)
- to place in the trim step after trimming, dereplication, pre-clustering and chimera removal
- disable the length truncation for 454 reads (no keepfirst option in trim.seqs, no -t in FlowClus) if only ITS1 or ITS2 region is extracted
- warning for the documentation: better not use with cd-hit-est clustering if only ITS1 or ITS2 region is extracted because those regions are highly variable in size and cd-hit-est always sort longest reads first, with the consequence that the first read used to create OTU seeds will not be the most abundant.
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In GitLab by @lentendu on Mar 21, 2018, 18:20
mentioned in commit d29b00b
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In GitLab by @lentendu on Mar 22, 2018, 13:44
mentioned in commit dc8fcd4
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Related Issues (20)
- Adapt raw stat R scripts to R 4
- Avoid error if all reads already used in one direction for bidirectionnal libraries
- Allow different set of parameters for checkpointing
- Add header option to mimato
- Add NGmerge as alternative pair-end algorithm
- Allow disabling DADA2 bimera removal HOT 1
- Problem with restart from step when cut_db in the steps
- Problem with cutadapt and anchored adapters
- Feature: similarity based clustering for pair-end sequences which cannot be assembled
- Feature: provide manually curated reference sequences to use for taxonomic identification
- More systematic compression at all levels
- Change minimum number of rank depending on database for cut_db
- Issue with ASV and swarm clustering not accepting N's
- Add version and commit number in env for backward compatibility
- Cluster with multiple previous sub-projects
- Force analyses for unpairable datasets
- Accept gz compress database fasta files
- Set a minimum amount of raw reads found in one orientation to consider this orientation
- Force all samples to belong to the same run for ASV error modl building
- Feature: allow to re-use same optimize quality parameters than a previous subproject
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