Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. — Wikipedia

A curated list of awesome Bioinformatics pipelines and software available on LatchBio. Command line or programmatic tools are now with Graphical User Interface and can be run without the hassle of software installation! Please feel free to contribute!

• Genome Assembly
  • De novo
  • Metrics
• Multiple sequence alignment
  • Align
  • Trimming
  • Summary statistics
• Phylogenetics
  • Phylogenetic inference
• Codon analyses
  • Optimization
• Contributors

• shasta
  wf.shasta | latch source code | paper-2020 | documentation
  • Rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input.

• BioKIT genome assembly metrics
  wf.genome_assembly_metrics_biokit | paper-2022 | documentation
  • Calculate diverse summary statistics for a genome assembly using BioKIT

• MAFFT
  wf.align_sequences_mafft | paper-2013 | documentation)

  • Multiple sequence alignment program.

• CIAlign
  wf.CIAlign | Paper | Documentation

  • Clean, visualise, and interpret multiple sequence alignment.

• ClipKIT
  wf.clipkit | paper-2020 | documentation
  • Multiple sequence alignment trimming for accurate phylogenomic inference.

• BioKIT alignment_summary_statistics
  wf.alignment_summary_statistics | paper-2022 | documentation
  • Calculate diverse summary statistics for a multiple sequence alignment using BioKIT

• IQ-TREE2
  wf.infer_phylogeny | paper-2020 | documentation
  • Efficient software for phylogenomic inference.

• BioKIT gRSCU
  wf.codon_optimization_biokit | paper-2022 | documentation
  • Estimate codon optimization using BioKIT

• CRISPRbuilderTB
  wf.CRISPRbuilderTB | Paper | documentation
  • Reconstruct Mycobacterium tuberculosis CRISPR-Cas loci from short reads using CRISPRbuilder-TB