Alternatives and similar repositories for SARS-CoV-2_Sequencing

Users that are interested in SARS-CoV-2_Sequencing are comparing it to the libraries listed below

• fbreitwieser / pavian
  🌈 Interactive analysis of metagenomics data
  ☆422Updated 3 weeks ago
• lh3 / bioawk
  BWK awk modified for biological data
  ☆627Updated 3 years ago
• broadinstitute / viral-ngs
  [THIS REPO IS DEPRECATED] see newer repos: https://github.com/broadinstitute/viral-core https://github.com/broadinstitute/viral-assemble …
  ☆196Updated 11 months ago
• ababaian / serratus
  Ultra-deep search for novel viruses
  ☆273Updated 2 years ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆527Updated last year
• chanzuckerberg / shasta
  [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
  ☆274Updated 2 years ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆265Updated 2 months ago
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆395Updated 3 months ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆353Updated last week
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆319Updated 6 months ago
• ablab / quast
  Genome assembly evaluation tool
  ☆458Updated 9 months ago
• ncbi / amr
  AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…
  ☆321Updated 2 weeks ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆425Updated this week
• bcgsc / abyss
  Assemble large genomes using short reads
  ☆323Updated 5 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆239Updated 4 years ago
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆380Updated last month
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆290Updated 4 months ago
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆369Updated last year
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆233Updated 2 years ago
• mummer4 / mummer
  Mummer alignment tool
  ☆525Updated 6 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆214Updated last year
• genometools / genometools
  GenomeTools genome analysis system.
  ☆321Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆368Updated 3 years ago
• bactopia / bactopia
  A flexible pipeline for complete analysis of bacterial genomes
  ☆468Updated 2 weeks ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆361Updated last month
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆524Updated last month
• tseemann / snippy
  Rapid haploid variant calling and core genome alignment
  ☆542Updated last year
• schatzlab / genomescope
  Fast genome analysis from unassembled short reads
  ☆295Updated last year
• whatshap / whatshap
  Read-based phasing of genomic variants, also called haplotype assembly
  ☆380Updated 2 months ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆252Updated last year