Alternatives and similar repositories for snp-sites:

Users that are interested in snp-sites are comparing it to the libraries listed below

• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆318Updated 10 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆357Updated 3 years ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆211Updated last year
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆307Updated last year
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆327Updated last year
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆248Updated last month
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆221Updated 2 years ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆334Updated last year
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆240Updated last year
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆201Updated 2 years ago
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆222Updated 2 years ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆302Updated last week
• MrOlm / drep
  Rapid comparison and dereplication of genomes
  ☆282Updated this week
• jtlovell / GENESPACE
  ☆204Updated 2 months ago
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆187Updated last year
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆346Updated last month
• nf-core / mag
  Assembly and binning of metagenomes
  ☆232Updated last week
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆276Updated 6 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆226Updated 4 years ago
• AdmiralenOla / Scoary
  Pan-genome wide association studies
  ☆193Updated 10 months ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆240Updated last year
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆376Updated 2 weeks ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆266Updated 2 months ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆239Updated last year
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆253Updated 3 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆288Updated 6 months ago
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆342Updated 2 years ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆257Updated 5 months ago
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆134Updated 2 years ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆501Updated last year