Alternatives and similar repositories for socru:

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

• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆57Updated last week
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆57Updated last month
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆23Updated 3 weeks ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆27Updated 5 months ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆48Updated 11 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated last week
• bvalot / pyMLST
  whole genome MLST analysis
  ☆41Updated last week
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated 3 years ago
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆24Updated 6 years ago
• LomanLab / EBAME18
  Long read metagenomics practical at EBAME18
  ☆18Updated 6 years ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆33Updated last month
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated last month
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
  ☆44Updated 3 weeks ago
• labgem / PlaScope
  Plasmid exploration of bacterial genomes
  ☆18Updated 3 years ago
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆25Updated 2 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 8 months ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆30Updated 5 years ago
• wandreopoulos / deeplasmid
  ☆20Updated 6 months ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆27Updated last year
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated last month
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 3 months ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆38Updated 5 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆33Updated 4 months ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆48Updated 2 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆71Updated last year