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

• broadinstitute / viral-ngs
  [THIS REPO IS DEPRECATED] see newer repos: https://github.com/broadinstitute/viral-core https://github.com/broadinstitute/viral-assemble …
  ☆195Updated last year
• lh3 / bioawk
  BWK awk modified for biological data
  ☆637Updated 3 years ago
• fbreitwieser / pavian
  🌈 Interactive analysis of metagenomics data
  ☆437Updated 3 months ago
• chanzuckerberg / shasta
  [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
  ☆274Updated 3 years ago
• bcgsc / abyss
  Assemble large genomes using short reads
  ☆329Updated 9 months ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆456Updated 2 years ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆362Updated last month
• nanopore-wgs-consortium / NA12878
  Data and analysis for NA12878 genome on nanopore
  ☆398Updated 3 years ago
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆378Updated last year
• artic-network / artic-ncov2019
  ARTIC nanopore protocol for nCoV2019 novel coronavirus
  ☆171Updated 2 years ago
• ablab / quast
  Genome assembly evaluation tool
  ☆489Updated last year
• tseemann / snippy
  Rapid haploid variant calling and core genome alignment
  ☆558Updated 3 weeks ago
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆400Updated 3 weeks ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆546Updated last year
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆516Updated last month
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆373Updated 3 years ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆261Updated last year
• nextstrain / nextclade
  Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
  ☆250Updated this week
• ababaian / serratus
  Ultra-deep search for novel viruses
  ☆275Updated 2 years ago
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆262Updated 2 years ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆243Updated 4 years ago
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆298Updated 8 months ago
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆247Updated 3 weeks ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆269Updated 6 months ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆374Updated this week
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆630Updated 3 weeks ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆217Updated 2 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆557Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆278Updated 2 years 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