Alternatives and similar repositories for quasitools

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

• metagentools / VStrains
  VStrains is a de novo approach for reconstructing strains from viral quasispecies.
  ☆23Updated 6 months ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• HaploConduct / HaploConduct
  Haplotype-aware genome assembly toolkit
  ☆30Updated 5 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• SamStudio8 / gretel
  An algorithm for recovering haplotypes from metagenomes
  ☆31Updated 4 years ago
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆36Updated last week
• sgearle / bugwas
  Locus and lineage tests for bacterial GWAS
  ☆29Updated 7 years ago
• Gardner-BinfLab / deltaBS
  Quantifying the significance of genetic variation using probabilistic profile-based methods.
  ☆19Updated 4 years ago
• hzi-bifo / Haploflow
  ☆31Updated last year
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆25Updated 2 years ago
• pierrepeterlongo / back_to_sequences
  ☆44Updated last month
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆46Updated 2 years ago
• iqbal-lab-org / make_prg
  Code to create a PRG from a Multiple Sequence Alignment file
  ☆25Updated 2 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆53Updated 4 months ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆62Updated 5 years ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated last week
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• dhelekal / CaveDive
  ☆17Updated last year
• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆38Updated 2 months ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated last year
• SwingOlive / kASA
  kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding
  ☆23Updated 2 years ago
• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆59Updated 4 years ago
• marbl / MetaCompass
  MetaCompass: Reference-guided Assembly of Metagenomes
  ☆39Updated 3 weeks ago
• dayzerodx / counterr
  ☆31Updated last year
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆35Updated 4 months ago
• gtonkinhill / pairsnp
  A set of scripts for calculating pairwise SNP distance
  ☆42Updated 2 years ago
• HaploKit / Strainline
  Full-length de novo viral haplotype reconstruction from noisy long reads
  ☆20Updated last year