Glossary

Apptainer

Container runtime used by Sequana pipelines (formerly known as Singularity). Images are pulled on demand via --use-apptainer.

BAI

Index file accompanying a BAM file (non-standard extension .bai).

BAM

Binary version of the SAM alignment format.

BED

Tab-separated format describing genomic intervals (chrom, start, end, plus optional fields). Used for coverage reporting.

CIGAR

Compact string describing how a read aligns to a reference (matches, insertions, deletions, soft-clips, …).

Conda environment

Isolated Python + binary environment managed by conda/mamba. Recommended for installing Sequana to avoid clashing with system packages.

DEG

Differentially Expressed Gene. Output of RNA-seq differential expression analyses (see sequana.rnadiff).

DSRC

A compression tool dedicated to FastQ files.

FASTA

Plain-text format for nucleotide or protein sequences. Each record starts with a > header line, followed by one or more sequence lines.

FASTQ

Plain-text format combining a sequence with per-base quality scores. Typically gzipped (.fastq.gz).

GFF

General Feature Format. Tab-separated annotation file describing genes, exons and other features along a sequence. See also GFF3.

GTF

Gene Transfer Format. Tab-separated annotation similar to GFF but with stricter attribute conventions.

JSON

Human-readable data serialisation language commonly used for configuration. See https://en.wikipedia.org/wiki/JSON.

k-mer

Substring of fixed length k from a sequence. Used in classification (Kraken), assembly (de Bruijn graphs), and quality control.

Module

A directory that contains a Snakemake rule and an associated README. Especially relevant for the Sequana pipelines. See Developer guide.

MultiQC

Aggregates outputs of many bioinformatics tools (FastQC, samtools, cutadapt …) into a single interactive HTML report. Sequana ships plugins for several of its pipelines.

NGS

Next-generation sequencing. Catch-all term for high-throughput sequencing technologies (Illumina, PacBio, ONT …).

Rule

Smallest unit of a Snakemake workflow: declares input, output, and the shell/Python code that turns one into the other.

SAM

Sequence Alignment Map. Tab-separated format describing read alignments to a reference.

Sample sheet

Tabular description of an Illumina run (sample IDs, indices, adapters). Parsed by sequana.iem.SampleSheet.

Snakefile

A file that contains one or several Snakemake rules.

Snakemake

Python-based workflow engine used by every Sequana pipeline.

Taxon

A taxonomic unit (species, genus, …) referenced by an NCBI taxid. Sequana's sequana.taxonomy loads the NCBI taxonomy dump.

VCF

Variant Call Format, used by the variant calling pipeline.

Wrapper

Reusable Snakemake rule shipped by sequana-wrappers and consumed by every pipeline via Snakemake's native wrapper: directive.

YAML

Human-readable data serialisation language commonly used for configuration files. Every Sequana pipeline configuration is YAML.