Alternatives and similar repositories for sepia:

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

• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆75Updated last month
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆43Updated 4 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆62Updated 2 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆57Updated last year
• rhysnewell / Lorikeet
  Strain resolver for metagenomics
  ☆72Updated 7 months ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated 10 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 2 years ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆56Updated last week
• Ivarz / Conifer
  Calculate confidence scores from Kraken2 output
  ☆21Updated last year
• combogenomics / medusa
  A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.
  ☆44Updated 4 years ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆28Updated 8 months ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago
• marbl / harvest
  ☆52Updated 3 years ago
• bede / hostile
  Precise host read removal
  ☆89Updated 2 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 this week
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 8 months ago
• katerinakazantseva / strainy
  Graph-based assembly phasing
  ☆74Updated 4 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆48Updated 7 months ago
• hcdenbakker / GTDB_Kraken
  Kraken(2) database based on the GTDB project
  ☆27Updated 6 years ago
• OLF-Bioinformatics / VariantDetective
  Identify short variants and structural variants from raw sequencing data or genomic sequences
  ☆25Updated 11 months ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆70Updated last year
• wdecoster / nanolyse
  Remove lambda phage reads from a fastq file
  ☆29Updated 2 years ago
• rrwick / Minipolish
  A tool for Racon polishing of miniasm assemblies
  ☆73Updated 3 years ago