repgenerate

• 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.
     ************************************************
     Author Gaurav Sablok,
     Email: codeprog@icloud.com
    ************************************************

Usage: repgenerate <COMMAND>

Commands:
multiplex  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

Gaurav Sablok
codeprog@icloud.com