Inspired by Awesome Pipeline
- Brisk - Exact resource-efficient dictionary for k-mers.
- digest - Fast and flexible minimizer digestion with digest.
- ModDotPlot - Rapid and interactive visualization of complex repeats.
- sTELLeR - Detecting transposable elements in long-read genomes.
- TeloSerachLR - telomere search using long sequencing reads.
- telescope - Single locus resolution of Transposable ELEment expression.
- teloscope - A universal telomere annotation tool for genome assemblies.
- TE-seq - A Transposable Element Annotation and RNA-Seq Pipeline.
- HiTE - Transposable Elements detection
- TEtrimmer - Manual curation of TEs.
- TEnest - TEnest.
- MCHelper - Curates transposable element libraries.
- SVbyEye A visual tool to characterize structural variation among whole genome assemblies. Genome aligners
- FastGA - A Fast Genome Aligner.
- gfatools - Processing pangenome alignments.
- Gretl - Gretl—variation graph evaluation TooLkit.
- Pandagma - A tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole genome duplications.
- Pangene - Constructing a pangenome gene graph.
- mumemto - finding multi-MUMs and MEMs in pangenomes.
- multi-MUMs - Improved pangenomic classification accuracy with chain statistics.
- reseek - Protein structure alignment by Reseek improves sensitivity to remote homologs.
- Evo - Sequence modeling and design from molecular to genome scale with Evo.
- FoldMason - Multiple Protein Structure Alignment at Scale with FoldMason.
- List of papers about protein design and deep leaning
- gget - querying of genomic reference databases.
- MSAplot - MSA visualization.
- tangermeme - Implementations of FIMO and TOMTOM.
- dSQ - Submit Job Arrays with dSQ
- Awesome-genome-vizualization - Collections of visualizations.