Alternatives and similar repositories for CSIS

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

• rrwick / Verticall
  Recombination-free trees
  ☆59Updated 4 months ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆73Updated last year
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆49Updated last year
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆34Updated 5 years ago
• Serka-M / mmlong2
  Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
  ☆49Updated 2 weeks ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆37Updated 2 months ago
• denglab / SeqSero2
  SeqSero2
  ☆38Updated last year
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆72Updated last month
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆49Updated 2 months ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆43Updated 2 weeks ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆61Updated last week
• LomanLab / EBAME18
  Long read metagenomics practical at EBAME18
  ☆18Updated 6 years ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆50Updated 6 months ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆46Updated last month
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆60Updated last month
• labgem / PlaScope
  Plasmid exploration of bacterial genomes
  ☆18Updated 3 years ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆40Updated 5 years ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆60Updated 5 months ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆30Updated 9 months ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆36Updated 3 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated last week
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆95Updated 10 months ago
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆74Updated last year
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆46Updated 4 years ago
• BU-ISCIII / plasmidID
  PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…
  ☆41Updated 4 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆25Updated 4 months ago