Filter 454 Reads

Filters 454 reads similarly to Hurwitz & Sullivan, 2013.

Remove sequences with ambiguous bases.
Remove sequences more than 2 standard deviations from the mean read length.

Installation

Precompiled binaries

This program is written in Rust. If you aren't familiar with compiling Rust programs and you are on Linux or Mac, you can just download the precompiled binaries and use those instead!

From source

Get the source code

git clone https://github.com/mooreryan/filter_454.git

cd into the directory

cd filter_454

Build the executable program with cargo. This command will use 8 CPUs. Change --jobs flag to the number of CPUs you want to use.

cargo build --release --jobs 8

The binary will be target/release/filter_454. You can now add the binary to somewhere on your path. I like to put a symlink to the executable file in ~/bin. You can do it like this.

ln -s $PWD/target/release/filter_454 $HOME/bin/filter_454

Usage

Here is an example command

filter_454 seqs.fa > seqs.filtered.fa