Sequence Data Formats & FAIR Interoperability — Hands-on

Gain expertise in sequence data formats and FAIR interoperability through hands-on parsing, validation, indexing, and standards-based packaging.

Sequence Data Formats & FAIR Interoperability

Session Index

Session 1

Fee: Rs 6300

Core Formats, Parsing & Compression

Essentials: FASTA, FASTQ, GFF3, BED, VCF field semantics

Theory

Efficient parsing & streaming pipelines

seqkit seqtk awk/sed pandas

Compression & binary formats

bgzip tabix BCF CRAM

Session 2

Fee: Rs 8400

FAIR, Schemas & Packaging

FAIR principles, provenance & minimal information checklists

FAIR MINSEQE MIxS

Schemas & semantic representations

JSON/JSON-LD RO-Crate DCAT

FAIR packaging & machine-actionable metadata

crate.json provenance licenses

Session 3

Fee: Rs 11200

Validation, QC & Indexing

Schema checks, field-level validation & repair

vcftools bcftools gffread bedtools

Checksums, integrity & reproducible data movement

sha256sum md5sum rsync

Indexing for scale & random access

tabix samtools index faidx

Session 4

Fee: Rs 14000

Mini Capstone: Interoperable Data Package

Design interoperable workflow & artifact structure

Theory

RO-Crate build with provenance & licenses

RO-Crate crate.json JSON-LD

Snakemake-based reproducible pipeline & deposit-ready bundle

Snakemake Conda/Mamba MultiQC

PDF

Sequence Data Formats & FAIR Interoperability Training | Parsing, Validation, RO-Crate Packaging