Alternatives and similar repositories for strainy:

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

• epi2me-labs / wf-16s
  ☆29Updated 3 months ago
• bcgsc / ntSynt
  Detecting multi-genome synteny using minimizer graph mapping
  ☆76Updated 2 months ago
• bcgsc / ntEdit
  ✏️ Genome assembly polishing & SNV detection
  ☆68Updated last month
• bcgsc / ntJoin
  🔗Genome assembly scaffolder using minimizer graphs
  ☆83Updated 6 months ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• mourisl / centrifuger
  Classifier for metagenomic sequences using FM-index with run-block compressed BWT.
  ☆56Updated 2 weeks ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆76Updated last month
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• daewoooo / SVbyEye
  ☆77Updated last month
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆41Updated this week
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆40Updated 4 months ago
• ksahlin / isONclust
  De novo clustering of long transcript reads into genes
  ☆59Updated 3 years ago
• bcgsc / LongStitch
  Correct and scaffold assemblies using long reads
  ☆50Updated last year
• Serka-M / Digester-MultiSequencing
  Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing
  ☆21Updated 2 years ago
• NBISweden / aMeta
  Ancient microbiome snakemake workflow
  ☆23Updated 3 months ago
• PacificBiosciences / pbtk
  PacBio BAM toolkit
  ☆41Updated last month
• marschall-lab / panacus
  Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
  ☆100Updated 2 weeks ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated 11 months ago
• nanoporetech / pipeline-umi-amplicon
  Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
  ☆33Updated last year
• Adamtaranto / teloclip
  A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
  ☆35Updated last week
• EBI-Metagenomics / mobilome-annotation-pipeline
  ☆41Updated this week
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• epi2me-labs / wf-alignment
  ☆27Updated last month
• yeeus / GCI
  A program for assessing the T2T genome continuity
  ☆69Updated 3 weeks ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• Gaius-Augustus / TSEBRA
  TSEBRA: Transcript Selector for BRAKER
  ☆47Updated 4 months ago
• DecodeGenetics / Ratatosk
  Hybrid error correction of long reads using colored de Bruijn graphs
  ☆100Updated 6 months ago
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆60Updated 2 years ago