alneberg/umi-transfer

A Rust software to extract Unique Molecular Identifiers in FastQ files and embedd them into the ID of the corresponding reads.

Building

Go to the directory with the tool and type in cargo build .

Running

Usage

The tool requires an input as follows:

umi-transfer [OPTIONS] <SUBCOMMAND>

OPTIONS:

Flag	Required	Description
-h,--help	No	Print help information
--prefix	No, but default will be 'integrated'	dictates name of output files
--r1-in	Yes	FASTQ file with reads
--r2-in	No	FASTQ file with reads

SUBCOMMANDS:

inline:

Flag	Required	Description
--pattern1	Yes	Nucleotide Pattern for UMI
--pattern2	Needed if --r2-in exists	Nucleotide Pattern for UMI

separate:

Flag	Required	Description
--ru-in	Yes	FASTQ containing UMI records

Running the tool can be done by cargo run --release -- [options] --r1-in 'fastq' <Subcommands> , where the --release flag is optional, but will ensure an optimized build.

Inline UMI example:

cargo run --release -- --prefix 'output' --r1-in 'R1.fastq' --r2-in 'R2.fastq' inline --pattern1 'NNNNNNNNN' --pattern2 'NNNNNNNNN'

UMI in seperate file example:

cargo run --release -- --prefix 'output' --r1-in 'R1.fastq' --r2-in 'R3.fastq' separate --ru-in 'R2.fastq'

Special flags:

--edit-nr This flag will automatically change the '3' in the R3 files record-headers. Its disabled by default. --no-gzip This flag diables automatic compression (.gz) of output files.