SeqSizzle is a pager for viewing FASTQ files with fuzzy matching, allowing different adaptors to be colored differently.

Installation

Pre-built binary

You can simply download and run the binary from Github Actions.

Conda

SeqSizzle is also available on bioconda:

conda install -c bioconda -c conda-forge seqsizzle

Cargo (crates.io)

If you already have a Rust environment set up, you can use the cargo install command:

cargo install seqsizzle

Cargo will build the seqsizzle binary and place it in $HOME/.local/share/cargo/bin/seqsizzle.

Cargo (git)

If you already have a Rust environment set up, you can use the cargo install command in your local clone of the repo:

git clone https://github.com/ChangqingW/SeqSizzle
cd SeqSizzle
cargo install --path .

Cargo will build the seqsizzle binary and place it in $HOME/.cargo.

Usage

./seqsizzle -h:

Usage: seqsizzle [OPTIONS] <FILE> [COMMAND]

Commands:
  summarize  Summarize the reads with patterns specified by the --patterns argument or the adapter flags. Make sure you supply the flags BEFORE the subcommand, e.g. `./SeqSizzle my.fastq -p my_patterns.csv --adapter-3p summarize`. '..' indicats unmatched regions of positive length, '-' indicates the patterns are overlapped, print the number of reads that match each pattern combination in TSV format. To be moved to the UI in the future
  help       Print this message or the help of the given subcommand(s)

Arguments:
  <FILE>  The FASTQ file to view

Options:
      --adapter-3p
          Start with 10x 3' kit adaptors:
           - Patrial Read1: CTACACGACGCTCTTCCGATCT (and reverse complement)
           - Partial TSO: AGATCGGAAGAGCGTCGTGTAG (and reverse complement)
           - Poly(>10)A/T
      --adapter-5p
          Start with 10x 5' kit adaptors
           - Patrial Read1: CTACACGACGCTCTTCCGATCT (and reverse complement)
           - TSO: TTTCTTATATGGG (and reverse complement)
           - Patrial Read2: AGATCGGAAGAGCACACGTCTGAA (and reverse complement)
           - Poly(>10)A/T
  -p, --patterns <PATTERNS_PATH>
          Start with patterns from a CSV file
          Must have the following header:
          pattern,color,editdistance,comment
  -s, --save-patterns <SAVE_PATTERNS_PATH>
          Save the search panel to a CSV file before quitting. To be removed in the future since you can now hit Ctrl-S in the search panel to save the patterns
  -h, --help
          Print help
  -V, --version
          Print version

Navigation

Viewer mode

Up / down arrow (or j / k) to scroll by one line, Ctrl+U / Ctrl+D to scoll half a screen.
/ (or Ctrl+F) to toggle search panel, q to quit

search panel mode

Left / right arrow (or Tab / Shift-Tab) to cycle through different input fields and the patterns list.
When on the patterns list field, up / down arrows cycle through patterns, Backspace (or Delete, d) to delete the selected pattern and Return to pop the pattern into the input fields for editing.
Return to add current inputs into the search pattern list (when focusing on any of the input boxes, rather than the patterns list).
Use Shift + arrow keys to move cursor within an input field (as arrow keys alone are bind to cycling input fields).
/ or Esc to close the search panel.

Roadmap

functionality

• Gzip (fastq.gz) support
• Filter reads by match
• Counting reads with match

UI

• Make elements in the search panel clickable, try implementations discussed in ratatui repo

Misc

• Unit tests