Seqsum

Warning

Seqsum was rewritten in Rust in 0.3.0. The original Python version of seqsum and how to use is archived in the python branch. It remains available on PyPI.

Robust checksums for nucleotide sequences. Accepts input from either standard input or fast[a|q][.gz|.zst] 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).

Install

cargo install seqsum

Development

git clone https://github.com/bede/seqsum.git
cd seqsum
cargo test

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