Comments (3)
One possibility could be the following structure:
{outdir}
├── final_output
│ └── illumina / nanopore / pacbio # one directory for each sequencing technology
│ │ └── all reads in ".fq.gz" format
├── preprocessing_outputs
│ └── illumina / nanopore / pacbio # one directory for each sequencing technology
│ │ └── QC, trimming, filtering, correction, demultiplexing etc. (whenever available)
# files of all samples will be placed inside the QC, trimming, filtering, etc directories. Each file will have the sample ID to make selection easier.
What do you think about such structure, @gpappasunb?
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I will also take advantage of the changes, to also change the software used for illumina preprocessing ---
Instead of using 4 different tools (fastqc, trim_galore, lighter and flash) I will use only fastp which has all the functionalities of these 4 tools and is much faster since it is written in C++
from ngs-preprocess.
The change to fastp
has already been addressed. The documentation needs to be properly changed prior to making a new release (v2.4).
Now, with fastp
and following the new structure of outputs, it would look like this:
TESTE
├── final_output
│ ├── illumina
│ │ ├── SRR8482585_30X.merged.fq.gz
│ │ ├── SRR8482585_30X_R1.unmerged.fq.gz
│ │ └── SRR8482585_30X_R2.unmerged.fq.gz
│ ├── nanopore
│ │ └── kp_30X.filtered.fq.gz
│ └── pacbio
│ └── lima.bc1018--bc1018.filtered.fq.gz
└── preprocessing_outputs
├── illumina
│ ├── SRR8482585_30X_fastp.html
│ └── SRR8482585_30X_fastp.json
├── nanopore
│ ├── QC
│ │ ├── kp_30X_nanoQC
│ │ ├── kp_30X_nanoplot
│ │ └── kp_30X_stats
│ └── porechop
│ └── kp_30X.trimmed.fq.gz
└── pacbio
├── QC
│ ├── lima.bc1018--bc1018_nanoQC
│ ├── lima.bc1018--bc1018_nanoplot
│ └── lima.bc1018--bc1018_stats
└── bam2fastq
├── lima.bc1018--bc1018.bam.pbi
└── lima.bc1018--bc1018.fq.gz
All these changes are already available in branch develop
and are being tracked by the draft PR #9.
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Related Issues (13)
- Add more parallel jobs HOT 1
- standard profile to not load docker
- Suggestion for hybrid error correction HOT 1
- fix bam2fastq source code HOT 1
- update module to fetch data from sra
- Change software for filtering longreads
- add citation information
- Enhance documentation (paper review) HOT 1
- Add example of non-bacterial dataset analysis (paper review) HOT 2
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