bigseq

A port of the BIGSI database to the Seq language.

COVID sequence for benchmarking comes from https://www.ncbi.nlm.nih.gov/sra/ERX5420434[accn]

Team Members: Gabe Ramirez, Kaveri Nadhamuni, Charvi Gopal

Installation

1. Clone the repo.
2. Install Seq, ensuring that it is in your $PATH and that $LD_LIBRARY_PATH contains {seq_installation_directory}/lib/seq

/bin/bash -c "$(curl -fsSL https://seq-lang.org/install.sh)"

3. Install BIGSI's required libraries. See their docs.
4. Compile the bigseq binary.

cd bigseq
seqc build -release bigseq.seq -o=bigseq

5. Set SEQ_PYTHON to the output of python3 find.py.
6. Run bigseq.

Commands

• bloom <ctx_file> <out_file>: constructs a bloom filter
• build -b <bloom_file> -s <sample_name> ...: builds an index
• search <seq>: searches for a matching sample

Licenses

See licenses directory and report.