- repgenerate for illumina sequencing reports, hich will demultiplex and does all the report generation for any Illumina sequencing platform.
- you and demultiplex, or demultiplex and report generation and lastly you can generate report from already demultiplexed reads.
cargo build
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demultiplexing and repgenerate for human genomics.
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Gaurav Sablok, IBCH, PAN, Poznan, Poland,
https://portal.ichb.pl/laboratory-of-genomics/.
Email: gsablok@ibch.poznan.pl
Prof. Luiza Handschuh
Email: luizahan@ibch.poznan.pl.
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Usage: repgenerate <COMMAND>
Commands:
demultiplex demultiplex the illumina sequencing
dereport demultiplex and report generate
report report claibration
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
- To install windows version:
rustup component add llvm-tools
rustup target add x86_64-pc-windows-msvc
git clone https://github.com/IBCHgenomic/eVaiutilities.git
cd ensemblcov
cargo xwin build --target x86_64-pc-windows-msvc
- to demultiplex the reads and generate the report
./target/debug/repgenerate dereport BHMT5TDRX3 SampleSheet20250509_ICHB_RNAseq001.csv
- to just demultiplex the reads
./target/debug/repgenerate multiplex BHMT5TDRX3 SampleSheet20250509_ICHB_RNAseq001.csv
- to run the simple report generator where you have a folder of any number of the fastp reports and for each sample, it will prepare a single file with what is needed. With demultiplex options, it will prepare the same report.
./target/debug/repgenerate report sample-file
duplication-rate:"0.083112"
insert size peak insert size unknown adapter trimmed reads adapter trimmed bases 170 5455420 24376812 893347838
before filtering
before filtering total_reads total_bases q20_bases q30_bases q20_rate q30_rate read1_mean_length read2_mean_length gc_content
105961318 16000159018 15672173600 15065791642 0.979501 0.941603 151 151 0.449647
after filtering
total_reads total_bases q20_bases q30_bases q20_rate q30_rate read1_mean_length read2_mean_length gc_content
104626372 14908378954 14761963198 14354265840 0.990179 0.962832 142 142 0.440785
- Acknowledgements: MOSAIC platform, developed as part of the ECBiG-MOSAIC project (POIR.04.02.00-00-D017/20), co-financed by the European Regional Development Fund (ERDF) under the Smart Growth Operational Programme 2014-2020, Measure 4.2 for the development of modern research infrastructure in the science sector.
- Informal queries: Prof. Luiza Handschuh: luizahan@ibch.poznan.pl.
- Code related queries: Dr. Gaurav Sablok: gsablok@ibch.poznan.pl.
Gaurav Sablok Instytut Chemii Bioorganicznej Polskiej Akademii Nauk ul. Noskowskiego 12/14 | 61-704, Poznań Poland