From 569c2ba7e209be288c56c262decc3c3dafece037 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Mon, 5 Feb 2024 14:11:32 -0500 Subject: [PATCH] ran the readme through the markdown linter --- README.md | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 3a9d8d88..37457537 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -[![Crates.io](https://img.shields.io/crates/v/fasten)](https://crates.io/crates/fasten) - # Fasten +[![Crates.io](https://img.shields.io/crates/v/fasten)](https://crates.io/crates/fasten) + A powerful manipulation suite for interleaved fastq files. Executables can read/write to `stdin` and `stdout`, and they are compatible with the interleaved fastq format. This makes it much easier to perform streaming operations using unix pipes. @@ -9,7 +9,7 @@ This makes it much easier to perform streaming operations using unix pipes. ## Synopsis ### read metrics - + $ cat testdata/R1.fastq testdata/R2.fastq | \ fasten_shuffle | fasten_metrics | column -t totalLength numReads avgReadLength avgQual @@ -27,8 +27,6 @@ This makes it much easier to perform streaming operations using unix pipes. 800 8 100 19.53875 # No reads were actually filtered with cleaning, with --min-length=2 -_etc_ - ## Installation ### Installation from source @@ -43,7 +41,7 @@ After downloading, use the Rust executable `cargo` like so: All executables will be in the directory `fasten/target/release`. -_note_: there are some `Makefile` methods to help including +_note_: there are some `Makefile` methods to help including * `make all` to make the following * `make release` install fast executables @@ -51,10 +49,9 @@ _note_: there are some `Makefile` methods to help including * `make fasten/doc` compile lastest documents * `make clean` uninstall local binaries - ### Installation without `git` -You can also install Fasten straight from using the following command: +You can also install Fasten straight from using the following command: cargo install fasten @@ -71,7 +68,7 @@ All scripts accept the parameters, read uncompressed fastq format from stdin, an ## Documentation -Please see the inline documentation at https://lskatz.github.io/fasten/fasten +Please see the inline documentation at This documentation was built with `cargo docs --no-deps` @@ -121,4 +118,3 @@ that indicates that you are securing your analysis by "fasten"ing it (with a sil ## Acknowledgements Thank you Henk Den Bakker for many helpful discussions around Rust, helping me name this software, and many other things. -