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
  ☆57Updated last year
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆48Updated 10 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
• simonrharris / SKA
  Split Kmer Analysis
  ☆63Updated 2 years ago
• xthua / bacant
  This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.
  ☆20Updated last year
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆27Updated 2 months ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 7 months ago
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆44Updated 3 weeks ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 2 years ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated 3 weeks ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆56Updated last month
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆43Updated 4 years ago
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆60Updated last month
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆38Updated 4 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆32Updated 2 months ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆70Updated last year
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆55Updated 5 months ago
• AuReMe / emapper2gbk
  Convert GFF, fastas, annotation table and species name into Genbank.
  ☆14Updated 10 months ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆26Updated 3 months ago
• labgem / PlaScope
  Plasmid exploration of bacterial genomes
  ☆18Updated 2 years ago
• wandreopoulos / deeplasmid
  ☆19Updated 5 months ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 2 months ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆30Updated 5 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆40Updated 9 months ago
• denglab / SeqSero2
  SeqSero2
  ☆34Updated 10 months ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆41Updated 3 weeks ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆36Updated 2 months ago
• Serka-M / mmlong2
  Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
  ☆43Updated last week