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
  ☆440Updated 4 months ago
• lh3 / bioawk
  BWK awk modified for biological data
  ☆635Updated 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 …
  ☆193Updated last year
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆381Updated last year
• bcgsc / abyss
  Assemble large genomes using short reads
  ☆328Updated 10 months ago
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆402Updated 2 weeks ago
• artic-network / artic-ncov2019
  ARTIC nanopore protocol for nCoV2019 novel coronavirus
  ☆170Updated 2 years ago
• ablab / quast
  Genome assembly evaluation tool
  ☆488Updated last year
• chanzuckerberg / shasta
  [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
  ☆274Updated 3 years ago
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆298Updated 9 months ago
• ababaian / serratus
  Ultra-deep search for novel viruses
  ☆275Updated 2 years ago
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆250Updated last month
• nanopore-wgs-consortium / NA12878
  Data and analysis for NA12878 genome on nanopore
  ☆402Updated 3 years ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆284Updated 5 months ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆455Updated 2 years ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆441Updated last week
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆335Updated 11 months ago
• broadinstitute / seqr
  web-based analysis tool for rare disease genomics
  ☆200Updated this week
• ncbi / amr
  AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…
  ☆349Updated this week
• tseemann / snippy
  Rapid haploid variant calling and core genome alignment
  ☆561Updated last month
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆525Updated 3 weeks ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆269Updated 7 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆551Updated last year
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆364Updated 2 months ago
• bactopia / bactopia
  A flexible pipeline for complete analysis of bacterial genomes
  ☆496Updated last month
• The-Sequence-Ontology / Specifications
  GFF and GVF specification documents
  ☆219Updated last year
• genometools / genometools
  GenomeTools genome analysis system.
  ☆333Updated 2 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆244Updated 4 years ago
• mummer4 / mummer
  Mummer alignment tool
  ☆547Updated 11 months ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆284Updated last year