nsearch

NGS data processing command-line tool & library for the rest of us. Written in C++11.

Features

Database search

• Query a list of DNA/RNA/amino acid sequences in a database of your choice.

Read processing

• Merge forward and reverse (Illumina) short-read sequences.
• Filter (merged) sequences based on the number of expected errors.

File formats

Currently supported:

• FASTA (merging output, searching input)
• FASTQ (merging input, merging output, searching input)
• ALNOUT (searching output)
• CSV (searching output)

Gzipped input files (e.g. db.fasta.gz) are supported.

Library

Use the libnsearch components for your own bioinformatics pipeline.

Requirements

• cmake: Build system. On macOS, installation via homebrew is recommended: brew install cmake.
• (optional) zlib: Reading compressed file support (.gz). brew install zlib.

Build instructions

mkdir build
cd build
cmake -D CMAKE_BUILD_TYPE=Release ..
make

Usage

Invoke the nsearch binary in the build/nsearch directory.

Tests

Run the test in the build directory:

make check

Code Style

A .clang-format for ClangFormat file is provided in the repository.

Tested on

• linux_64, vc >= 14.2
• osx_64, libcxx >= 12.0.1
• win_64, libgcc-ng >= 10.3.0

Details available at https://anaconda.org/conda-forge/nsearch/files.