Frequently used commands in bioinformatics

Functional tests for command line applications

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

Using ChatGPT & GPT-4 to generate CRAM & PyCRAM designators in a one-shot fashion

Tool for copying read-alignments regions centered around variants (in VCF/VCF.GZ/BCF format) from existing genomes (in SAM/BAM/CRAM format) to concat them into canvas genomes (in SAM/BAM/CRAM format).

Machinekit configuration for the Fabrikator Mini + CRAMPS board

Tool for adding genomic variants to an existing genome (in SAM/BAM/CRAM format). Currently supported variants are SNVs, indels and SVs (insertions, deletions, translocations, inversions and duplications). It generates realistic genomes as almost always less than 99% of the original real genome is modified.

a REST service to launch pipeline

School project : Create the Cram game in Python with game display in the Python console.

Convert output from Cram (and some other tools) to TAP (Test Anything Protocol)

Computes per-sample coverage from multiple BAM, CRAM, or bedGraph files, ensuring each genomic position is counted only once per sample. Chromosomes are processed in parallel to maximize throughput, producing a single tabix-indexed bedGraph.gz file.