Alternatives and similar repositories for ComputationalGenomicsManual

Users that are interested in ComputationalGenomicsManual are comparing it to the libraries listed below

• ISUgenomics / bioinformatics-workbook
  Bioinformatics Workbook repository
  ☆204Updated last month
• franciscozorrilla / metaGEM
  An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within micro…
  ☆253Updated last year
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆401Updated 2 months ago
• jotech / gapseq
  Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
  ☆204Updated last week
• moshi4 / pyGenomeViz
  A genome visualization python package for comparative genomics
  ☆388Updated 2 months ago
• SvetlanaUP / A-microbiologist-wants-to-compute
  This repo collects the list of learning online resources related to microbiome computational science and tools.
  ☆103Updated last year
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆378Updated 2 weeks ago
• usadellab / Trimmomatic
  ☆286Updated 3 months ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆366Updated this week
• bactopia / bactopia
  A flexible pipeline for complete analysis of bacterial genomes
  ☆496Updated last month
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆455Updated last year
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆403Updated 3 weeks ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆365Updated 6 months ago
• inab / trimal
  A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
  ☆248Updated this week
• nextflow-io / training
  Nextflow training material
  ☆212Updated this week
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆245Updated 4 years ago
• WrightonLabCSU / DRAM
  Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
  ☆319Updated this week
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆285Updated 5 months ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆340Updated 10 months ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆441Updated 2 weeks ago
• usadellab / Helixer
  Using Deep Learning to predict gene annotations
  ☆275Updated this week
• shenwei356 / taxonkit
  A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
  ☆456Updated last month
• lh3 / miniprot
  Align proteins to genomes with splicing and frameshift
  ☆395Updated last month
• ebi-pf-team / interproscan
  Genome-scale protein function classification
  ☆364Updated last week
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆633Updated last month
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆364Updated last week
• iqtree / iqtree2
  IQ-TREE software version 2: phylogenetics by maximum likelihood
  ☆321Updated 9 months ago
• rnnh / bioinfo-notebook
  🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.
  ☆203Updated 5 years ago
• biobakery / humann
  HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
  ☆232Updated 2 weeks ago
• bioconvert / bioconvert
  Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
  ☆386Updated 7 months ago