Alternatives and similar repositories for lrge:

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

• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆41Updated last month
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆48Updated 6 months ago
• gbouras13 / pypolca
  Standalone Python re-implementation of the POLCA polisher from MaSuRCA
  ☆29Updated 4 months ago
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆31Updated 2 months ago
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆35Updated 3 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆19Updated 6 months ago
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆24Updated 9 months ago
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆19Updated 3 months ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆30Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆56Updated last year
• Sudaraka88 / LDWeaver
  Genomewide Epistasis Analysis on Bacteria
  ☆14Updated 4 months ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆25Updated 2 months ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆30Updated last month
• martinghunt / tna
  ☆12Updated last month
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆27Updated last year
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆20Updated 2 months ago
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…
  ☆41Updated 3 weeks ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆34Updated last month
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• pangenome / PanSN-spec
  Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
  ☆36Updated 3 months ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 6 months ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 2 months ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆34Updated last month
• mbhall88 / NanoVarBench
  Evaluating Nanopore-based bacterial variant calling
  ☆15Updated last month
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆26Updated 2 years ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆24Updated 3 months ago