mmatschiner / tutorials

Related projects ⓘ

Alternatives and complementary repositories for tutorials

• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆294Updated last year
• simonhmartin / genomics_general
  General tools for genomic analyses.
  ☆343Updated 3 months ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆382Updated this week
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆396Updated last year
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆213Updated 3 years ago
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆348Updated 2 months ago
• thackl / gggenomes
  A grammar of graphics for comparative genomics
  ☆602Updated 2 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆572Updated 6 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆276Updated last month
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆364Updated last week
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆323Updated 2 years ago
• Kinggerm / GetOrganelle
  Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)
  ☆275Updated 3 weeks ago
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆377Updated last month
• iqtree / iqtree2
  NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
  ☆246Updated this week
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆202Updated 11 months ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆452Updated this week
• picrust / picrust2
  Code, unit tests, and tutorials for running PICRUSt2
  ☆328Updated 3 months ago
• Nextomics / NextDenovo
  Fast and accurate de novo assembler for long reads
  ☆369Updated 6 months ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆322Updated 3 months ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆321Updated last year
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆232Updated 2 years ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆283Updated 3 weeks ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆473Updated 9 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆384Updated this week
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆257Updated last year
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆375Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆341Updated 2 years ago
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆293Updated 3 months ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆561Updated this week
• biobakery / biobakery
  bioBakery tools for meta'omic profiling
  ☆262Updated last month