Seqsum

Robust checksums for nucleotide sequences. Accepts input from either standard input or fast[a|q][.gz|.zst|.xz|.bz2] files. Generates individual checksums for each sequence, plus an aggregate checksum for a collection. Warnings are shown for duplicate sequences and within-collection checksum collisions at the selected bit depth. Sequences are uppercased before hashing with rapidhash (v3) and may be normalised (with -n) to use only ACGTN-. Read IDs and FASTQ base quality scores do not inform the checksum. Output is tab-delimited text to stdout.

By default, seqsum outputs individual checksums and, when there is more than one sequence, an aggregate checksum. This can be modified with --individual (-i) or --aggregate (-a).

Uses paraseq for efficient FASTA/FASTQ parsing.

Install

cargo install --path .

Development

git clone https://github.com/bede/seqsum.git
cd seqsum
cargo test
cargo fmt --all --check
cargo clippy --all-targets -- -D warnings

Command line usage

# Fasta with one record
$ seqsum tests/data/MN908947.fasta
33ba13564e0a63e3	MN908947.3

# Fasta with two records
$ seqsum tests/data/MN908947-BA_2_86_1.fasta
33ba13564e0a63e3	MN908947.3
9fef3b61d54d8902	BA.2.86.1
d3a94eb82357ece5	aggregate

# Fasta with two records, only show aggregate checksum
$ seqsum tests/data/MN908947-BA_2_86_1.fasta --aggregate
d3a94eb82357ece5	aggregate

# Fasta via stdin
$ cat tests/data/MN908947.fasta | seqsum -
33ba13564e0a63e3	MN908947.3

Built-in help

$ seqsum -h