andrewdavidsmith/adapto-rs

Remove adaptors from short-read bisulfite sequencing data (coded in rust)

adapto-rs

Remove adaptors from short-read sequencing data. I needed a faster tool to remove adaptor sequences from reads for my own in my own data analysis. I wrote this in Rust because I wanted to experiment with the libraries for parallelism. It turns out this application does not need much in the way of parallelism. I think this code is reasonably fast. Unlike the tools I was using previously, adapto-rs does not use more cores concurrently than the number of threads specified by the user, which is an absolute requirement of my computing environment.

If you have cargo installed, you can build this code by doing:

cargo build --release

in the root of the source directory, and then run

./target/release/adapto-rs

to see the command line arguments.

If you need a static linked binary, which I currently do for a cluster (x86, linux) environment that I do not manage, you can build one on your own Ubuntu machine by doing the following:

sudo apt install musl-tools
rustup target add x86_64-unknown-linux-musl
RUSTFLAGS='-C target-feature=+crt-static' cargo build --release --target x86_64-unknown-linux-musl

I think I got a smaller and possibly faster binary with this instead:

RUSTFLAGS='-C target-feature=+crt-static -C codegen-units=1 -C lto -C embed-bitcode=yes' cargo build --release --target x86_64-unknown-linux-musl

You will then find the binary in the ./target/x86_64-unknown-linux-musl/release/ subdirectory.