Alternatives and similar repositories for counterr

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

• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆50Updated 4 years ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆62Updated 5 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• HaploKit / Strainline
  Full-length de novo viral haplotype reconstruction from noisy long reads
  ☆20Updated last year
• LANL-Bioinformatics / PhaME
  Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…
  ☆33Updated last year
• xfengnefx / hifiasm-meta
  hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
  ☆68Updated 2 months ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• mdcao / npScarf
  ☆26Updated 5 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…
  ☆58Updated 4 years ago
• oma219 / spumoni
  Pan-Genomic Matching Statistics
  ☆53Updated last year
• rrwick / MinION-desktop
  Scripts and programs for the Holt Lab's MinION desktop
  ☆32Updated 4 years ago
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆73Updated last month
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆41Updated 4 years ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆53Updated 2 months ago
• marbl / harvest
  ☆53Updated 4 years ago
• sirselim / guppy_parameter_optimiser
  A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
  ☆30Updated 3 years ago
• Kirk3gaard / 2023-basecalling-benchmarks
  ☆30Updated last year
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆50Updated 3 years ago
• wdecoster / nanolyse
  Remove lambda phage reads from a fastq file
  ☆29Updated 2 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• UCSC-nanopore-cgl / MarginPolish
  MarginPolish: Graph based assembly polishing
  ☆46Updated 4 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆30Updated 9 months ago
• yangao07 / longcallD
  A local-haplotagging-based small and structural variant caller
  ☆80Updated 3 weeks ago
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆41Updated last month
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated 2 weeks ago
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆63Updated last year
• thackl / minidot
  Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
  ☆76Updated 9 years ago
• JensUweUlrich / ReadBouncer
  Fast and scalable nanopore adaptive sampling
  ☆34Updated 2 years ago