Alternatives and similar repositories for clean:

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

• jonas-fuchs / BAMdash
  create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
  ☆43Updated 6 months ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆36Updated this week
• Serka-M / Digester-MultiSequencing
  Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing
  ☆21Updated 2 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 2 months ago
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆33Updated 3 years ago
• CAMI-challenge / OPAL
  OPAL: Open-community Profiling Assessment tooL
  ☆28Updated last month
• OLF-Bioinformatics / VariantDetective
  Identify short variants and structural variants from raw sequencing data or genomic sequences
  ☆24Updated 11 months ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆82Updated 2 years ago
• EBI-Metagenomics / mettannotator
  ☆65Updated 2 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆57Updated last year
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• simonrharris / SKA
  Split Kmer Analysis
  ☆62Updated 2 years ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆28Updated 8 months ago
• davidemms / SHOOT
  SHOOT.bio - the phylogenetic search engine
  ☆24Updated last year
• wdecoster / nanolyse
  Remove lambda phage reads from a fastq file
  ☆29Updated 2 years ago
• nanoporetech / pipeline-umi-amplicon
  Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
  ☆33Updated last year
• santeripuranen / SpydrPick
  SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
  ☆13Updated 2 years ago
• ignasrum / hocort
  HoCoRT - Remove specific organisms from sequencing reads
  ☆17Updated last month
• bvalot / pyMLST
  whole genome MLST analysis
  ☆40Updated 9 months ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆61Updated 4 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆27Updated last year
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆31Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• jeffersonfparil / compare_genomes
  A comparative genomics workflow using Nextflow, conda, Julia and R
  ☆36Updated 10 months ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated 10 months ago
• metagenomics / denbi-nanopore-training
  de.NBI Nanopore Training Course
  ☆20Updated 2 years ago
• xfengnefx / hifiasm-meta
  hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
  ☆62Updated 2 months ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago