seqstatx 0.1.0

Fast sequence statistics for FASTA/FASTQ files — N50, GC%, length distributions and more

seqstats

Fast sequence statistics for FASTA and FASTQ files — works on plain or gzipped inputs, no dependencies.

file                            seqs      total_bp      gc%      mean_len    min_len   max_len   N50         N90
-----------------------------------------------------------------------------------------------------------------
GRCh38.primary_assembly.fa      194       3,088,286,401  40.93   15,918,992  970       248,956,422  153,373,213  40,103,529
SRR10045678_1.fastq.gz          10000000  1,510,000,000  50.21   151.0       151       151          151          151

Install

pip install seqstatx

Or for development:

git clone https://github.com/perhapsstrawberries/seqstats.git
cd seqstats
pip install -e .

Usage

# single file
seqstatx genome.fa

# multiple files, gzipped FASTQ
seqstatx sample1.fastq.gz sample2.fastq.gz

# TSV output for downstream parsing
seqstatx --tsv *.fa > stats.tsv

# pipe to column for alignment
seqstatx --tsv *.fastq.gz | column -t

Metrics

Column	Description
seqs	Number of sequences / reads
total_bp	Total base pairs
gc%	GC content (%)
mean_len	Mean sequence length
min_len / max_len	Shortest / longest sequence
N50	50% of total assembly is in sequences ≥ this length
N90	90% of total assembly is in sequences ≥ this length

Supported formats

Extension	Format
.fa .fna .fasta	FASTA
.fq .fastq	FASTQ
.fa.gz .fastq.gz etc.	gzipped variants

Why

Existing tools (seqkit, seqtk) are great but require installation of compiled binaries.
seqstats is pure Python 3.10+, zero dependencies, pip-installable from any HPC or Conda environment.

License

MIT