PipeConcord

pipeconcord compares bioinformatics pipeline outputs with semantic metrics instead of byte-for-byte snapshots. Each comparator returns the same ConcordanceReport shape, so one-off checks and batch regression tests can consume results consistently.

Rename note: the first alpha release used the package name biocompare. Current and future releases use pipeconcord to avoid confusion with an unrelated life-science product directory.

The documentation site is intended for users evaluating the project as a tool for regression testing, pipeline validation, and reproducible scientific comparisons.

Current Comparators

Type Inputs Main metrics
table CSV/TSV tables row overlap, numeric similarity, categorical agreement
deg differential expression tables significant set overlap, logFC correlation, direction agreement
counts gene-by-sample count matrices sample correlations, library ratios, zero-pattern overlap
expression TPM/FPKM/CPM matrices expression profile correlation, distribution similarity, top gene overlap
bed BED3+ intervals bp Jaccard, interval precision/recall/F1
fasta/fastq sequence records record overlap, exact sequence agreement, GC/length similarity
vcf VCF calls normalized allele Jaccard, genotype concordance, AF correlation, Ti/Tv
bam_stats samtools flagstat / samtools stats text alignment-rate, duplicate-rate, and count-ratio similarity

Common Commands

Install from PyPI:

python3 -m pip install pipeconcord

PyPI package: https://pypi.org/project/pipeconcord/

pipeconcord compare file_a.tsv file_b.tsv --type table --key gene_id
pipeconcord batch manifest.tsv --min-concordance 0.95
pipeconcord compare file_a.bed file_b.bed --type bed --format html --output report.html

Documentation

Source Repository