Alternatives and similar repositories for SPEAR

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

• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated 2 years ago
• CFIA-NCFAD / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆24Updated 2 weeks ago
• prophyle / prophyle
  Accurate, resource-frugal and deterministic DNA sequence classifier.
  ☆36Updated last week
• niemasd / ViralConsensus
  Fast viral consensus genome reconstruction
  ☆25Updated this week
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆24Updated 3 years ago
• treangenlab / Olivar
  Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
  ☆37Updated 2 weeks ago
• nodrogluap / nanostripper
  Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria
  ☆14Updated 4 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 6 years ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 3 years ago
• RIVM-bioinformatics / AmpliGone
  A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment
  ☆20Updated 2 months ago
• GuyBaele / SpreadGL
  Main development repository for SpreadGL
  ☆20Updated last year
• SwingOlive / kASA
  kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding
  ☆23Updated 2 years ago
• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• FOI-Bioinformatics / nanometa_live
  A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…
  ☆20Updated last year
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated 2 weeks ago
• snayfach / IGGsearch
  Metagenomic species profiling with enhanced coverage of the human gut microbiome
  ☆25Updated last year
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆26Updated 2 years ago
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆35Updated 4 years ago
• leoisl / bacterial_assembly_pipeline
  ☆11Updated last year
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated last year
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆33Updated last year
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆39Updated 11 months ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 5 months ago
• nebiolabs / VarSkip
  VarSkip multiplex PCR designs for SARS-CoV-2 sequencing
  ☆14Updated 3 years ago
• EvolBioInf / fur
  Find Unique genomic Regions
  ☆32Updated 2 weeks ago
• dib-lab / 2018-ncbi-lineages
  Extract lineage CSVs from NCBI for use with sourmash lca.
  ☆29Updated 2 years ago
• pmenzel / taxonomy-tools
  C++ tools for NCBI taxonomy tasks
  ☆12Updated 7 months ago
• eclarke / komplexity
  A method of assessing sequence complexity based on kmer frequencies
  ☆33Updated 7 years ago
• josephpetrone / RESCUE
  Resolving Species Level Classification Using Emu
  ☆14Updated last year
• fbreitwieser / card-krakendb
  Scripts for creating a Kraken database from the Comprehensive Antibiotic Resistance Database
  ☆10Updated 9 years ago