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Conclusion

You can now read the formats that carry most genomic data, and you've worked with each of them yourself. Together they follow an analysis from start to finish:

Compression and BGZF runs underneath almost all of them. A file that is sorted, compressed with BGZF and indexed lets a tool jump straight to one region, however large the file.

Keep Practicing​

Sandbox.bio runs real bioinformatics tools in your browser, and its tutorials pick up where this chapter leaves off.

For FASTQ files, Wrangle FASTA and FASTQ with SeqKit summarizes, subsamples, filters and searches reads with seqkit. DNA Sequencing QC checks the quality of a paired-end run, then trims and filters the reads, with fastp.

For SAM and BAM files, BAM Parsing with samtools converts SAM to BAM, sorts and indexes it, reads the header and uses the FLAG to pick out alignments.

For VCF files, Sequence Alignment with bowtie2 maps reads and, in its last step, calls variants with bcftools mpileup and bcftools call. The IGV tutorial loads read alignments into the IGV genome browser and shows how to tell real variants from artifacts.

For BED files, the bedtools tutorial uses bedtools on real BED files to find overlaps, merge nearby regions, find the gaps between regions and measure coverage.

What's Next​

That's the end of the main text. Congratulations on making it this far! You started with what a cell is, and you can now take a sample's reads all the way to its variants and read every file along the way.

If you'd like to keep going, Advanced Topics gathers standalone pages on subjects such as alternative splicing, epigenetic modifications and the structure of DNA. Read them in any order, whenever one interests you.

Thanks for reading!