nanocount

A CLI to map single-end reads to dual guide protospacers.

Built originally to map long-read nanopore sequences to dual guide protospacers in a error-tolerant manner (mismatch + indel).

Installation

Quick installation with cargo:

# Requires target-cpu=native for compilation
export RUSTFLAGS="-C target-cpu=native";

# Install via cargo
cargo install nanocount

# Check the CLI documentation
nanocount --help

From github:

# Clone the repository
git clone https://github.com/noamteyssier/nanocount.git
cd nanocount

# Install with cargo
cargo install --path .

# Check the CLI documentation
nanocount --help

Usage

This is expecting a BINSEQ file with a single sequence per record.

The expected structure is:

[...][protospacer_1][...][protospacer_2][...]

nanocount will count the number of occurences of each protospacer and the number of occurences of each pair of protospacers.

nanocount -p my_protospacers.tsv <input>.vbq

Protospacer input

The protospacer input should be a TSV (no header) with four columns:

1. Construct Name
2. Alias
3. Protospacer1 Sequence
4. Protospacer2 Sequence

Note: The sequences will be converted to uppercase before counting and will appear in uppercase in the output.

Output

The output will be a TSV (with header) with the following columns:

1. construct: Full construct name
2. alias: Alias of construct
3. g1: Protospacer1 Sequence
4. g2: Protospacer2 Sequence
5. count_g1: Number of sequences with Protospacer1
6. count_g2: Number of sequences with Protospacer2
7. count_paired: Count of sequences with both Protospacers
8. count_unpaired: Count of sequences with only one of the pairs

Configuration

nanocount uses sassy as the alignment engine.

You can control your match sensitivity with the -k flag, which specifies the maximum alignment score for a putative match.

Note: Only the protospacer sequences are being compared. This does not make any comparison on constant sequences before, between, or after the protospacers.

# Allow a maximum of 3 mismatches/indels
nanocount -k 3 -p my_protospacers.tsv <input>.vbq