Alternatives and similar repositories for Conifer

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

• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆64Updated 7 months ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆51Updated 4 years ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆36Updated 4 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆78Updated 4 months ago
• MicrobialDarkMatter / nanomotif
  Nanomotif - a tool for identifying methylated motifs in metagenomic samples
  ☆35Updated 2 months ago
• katerinakazantseva / strainy
  Graph-based assembly phasing
  ☆90Updated 2 months ago
• LomanLab / EBAME18
  Long read metagenomics practical at EBAME18
  ☆18Updated 7 years ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆103Updated 3 weeks ago
• rrwick / Verticall
  Recombination-free trees
  ☆63Updated 5 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆47Updated 3 months ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆63Updated last week
• simonrharris / SKA
  Split Kmer Analysis
  ☆67Updated 3 years ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆32Updated last month
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆33Updated 6 years ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆35Updated last year
• bvalot / pyMLST
  whole genome MLST analysis
  ☆50Updated 7 months ago
• bluenote-1577 / myloasm
  A new high-resolution long-read metagenome assembler for even noisy reads
  ☆120Updated this week
• LaborBerlin / ont-assembly-snake
  Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.
  ☆27Updated last year
• ksahlin / NGSpeciesID
  Reference-free clustering and consensus forming of long-read amplicon sequencing
  ☆66Updated 9 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆81Updated 3 years ago
• scwatts / hicap
  in silico typing of the H. influenzae cap locus
  ☆12Updated last year
• katholt / RedDog
  ☆37Updated 3 years ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆55Updated last year
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆68Updated 4 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆63Updated 9 months ago
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆32Updated 9 months ago
• andrewgull / MGERT
  Mobile Genetic Elements Retrieving Tool
  ☆16Updated 8 months ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆98Updated last week
• BU-ISCIII / plasmidID
  PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…
  ☆42Updated 4 years ago