Awesome LatchBio

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!

Table of Contents

• Genome Assembly
  • De novo
  • Metrics
  • Circular genomes
• Sequence alignment
  • BLAST
  • LAST
• Multiple sequence alignment
  • Align
  • Trimming
  • Summary statistics
• Phylogenetics
  • Phylogenetic inference
  • Bayesian evolutionary analysis
• Codon analyses
  • Optimization
• CRISPR
  • CRISPR locus
• RNA Design and Analysis
  • NUPACK
• General use
  • Latch console
• Contributors

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Genome Assembly

De novo

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

Metrics

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

Circular genomes

• Circlator
  github repo | paper-2015
  • Circlator is a post-assembly improvement toolkit for producing correctly represented circular DNA structures.

Sequence alignment

BLAST

• makeblastdb | Latch Workflow | Source Code | Documentation
  • Produce BLAST databases from FASTA files
• blast | Coming soon
  • Align biological sequences against other sequences or a database indexed with makeblastdb

LAST

• lastdb | Latch Workflow | Source Code | Related Papers | Documentation
  • Prepare sequences for subsequent comparison and alignment using lastal
• lastal | Latch Workflow | Source Code | Related Papers | Documentation
  • Find local alignments between query sequences, and reference sequences that have been prepared using lastdb.

Multiple sequence alignment

Align

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

  • Multiple sequence alignment program.

• CIAlign
  wf.CIAlign | Paper | Documentation

  • Clean, visualise, and interpret multiple sequence alignment.

Trimming

• ClipKIT
  wf.clipkit | paper-2020 | documentation

  • Multiple sequence alignment trimming for accurate phylogenomic inference.

• **CIAlign
  wf.CIAlign | Latch source code | Documentation

  • Clean, visualise, and interpret the multiple sequence alignment

Summary statistics

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

Phylogenetics

Phylogenetic inference

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

Bayesian evolutionary analysis

• BEAST | Latch Workflow | Source Code | Related Papers | Documentation
  • Bayesian analysis of molecular sequences using Monte Carlo Markov Chain

Codon analyses

Optimization

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

CRISPR

CRISPR locus

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

RNA Design and Analysis

NUPACK

• NUPACK Loop and Stack Energies | Latch Workflow | Source Code | Related Papers | Documentation

  • Analyse loop free energy and stacking state free energies for single and multiloop structures using NUPACK

• NUPACK - Utilities | Latch Workflow | Source Code | Related Papers | Documentation

  • Structural analysis using NUPACK Utilities for a complex formed between two nucleotide strands

General use

Latch console

• Downloader | Latch Workflow | Source Code
  • Download files directly in the Latch Console

Contributors