Alternatives and similar repositories for snp-sites

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

• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆242Updated 4 years ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆333Updated last month
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆354Updated 2 months ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆248Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆369Updated 3 years ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆326Updated 6 months ago
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆250Updated 3 years ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆271Updated 2 years ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆266Updated 4 months ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆208Updated 2 years ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆216Updated last year
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆237Updated 2 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆276Updated last month
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆373Updated last month
• nf-core / mag
  Assembly and binning of metagenomes
  ☆249Updated this week
• marbl / verkko
  Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…
  ☆365Updated last month
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆283Updated last year
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆270Updated 3 weeks ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆258Updated 2 years ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆366Updated 3 months ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆146Updated 10 years ago
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆416Updated 6 months ago
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆206Updated last year
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆215Updated 2 years ago
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆355Updated 3 years ago
• schatzlab / genomescope
  Fast genome analysis from unassembled short reads
  ☆299Updated last year
• TransDecoder / TransDecoder
  TransDecoder source
  ☆298Updated last month
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆319Updated 2 years ago
• alekseyzimin / masurca
  ☆267Updated 4 months ago
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆138Updated 3 years ago