Comments (3)
In GitLab by @lentendu on Jun 13, 2018, 15:42
changed the description
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In GitLab by @lentendu on Jun 13, 2018, 15:46
changed the description
from deltamp.
This should be implement with vsearch, implies no filtration on maximum homopolymer length (should not be an issue for Illumina reads).
Two possibilities when using --fastx_filter :
- --fastq_trunclen then fastq_maxee or --fastq_maxee_rate
- --fastq_truncee and --fastq_minlen
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Related Issues (20)
- Correct Phred score optimized quality value selection for no truncation
- Avoid any array script to fail when no more reads in the sample
- Check for missing samples at demultiplexing
- Illumina_demulti find in late array job drop errors for missing files removed by other arrays HOT 1
- Declare COMP and DECOMP in deltamp main
- Add average expected truncation parameter to force optimization to reads of expected length
- Allow for possibility to truncate only based on expected error HOT 1
- Replace OBITools and MOTHUR by seqkit and vsearch where possible
- Add configuration parameter to assign standard and large memory node to different partition names
- Simplify demultiplexing Illumina as cutadapt now supports parallel computation for demultiplexing
- 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
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