Alternatives and similar repositories for gretel:

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

• iqbal-lab-org / make_prg
  Code to create a PRG from a Multiple Sequence Alignment file
  ☆25Updated last year
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆30Updated last year
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 2 weeks ago
• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆30Updated 2 weeks ago
• HaploConduct / HaploConduct
  Haplotype-aware genome assembly toolkit
  ☆29Updated 5 years ago
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated last month
• Dmitry-Antipov / viralFlye
  viralFlye pipeline
  ☆18Updated 8 months ago
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆32Updated 4 months ago
• niemasd / ViralConsensus
  Fast viral consensus genome reconstruction
  ☆22Updated 4 months ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆45Updated 2 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆28Updated last year
• karel-brinda / Phylign
  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
  ☆32Updated last year
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆21Updated last year
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated last month
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 9 months ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆52Updated last week
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆41Updated 4 years ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago
• broadinstitute / StrainGE
  strain-level analysis tools
  ☆36Updated 6 months ago
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆29Updated 3 weeks ago
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆37Updated last month
• NickJD / ORForise
  Comparison pipeline for Prokaryote Protein Coding Gene Predictors
  ☆23Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• rrwick / Compare-annotations
  A script for comparing old vs new versions of genome annotations
  ☆20Updated last year
• mbhall88 / NanoVarBench
  Evaluating Nanopore-based bacterial variant calling
  ☆18Updated 4 months ago