Alternatives and similar repositories for BBMap

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

• TransDecoder / TransDecoder
  TransDecoder source
  ☆298Updated 3 weeks ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆354Updated 2 months ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆326Updated 6 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆282Updated 8 months ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆271Updated 2 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆276Updated last month
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆146Updated 10 years ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆366Updated 3 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆369Updated 3 years ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆333Updated last month
• usadellab / Trimmomatic
  ☆271Updated last week
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆373Updated last month
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆216Updated last year
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆270Updated 3 weeks ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆266Updated 4 months ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆277Updated 2 months ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆142Updated 3 months ago
• Nextomics / NextDenovo
  Fast and accurate de novo assembler for long reads
  ☆395Updated last year
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆374Updated last year
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆283Updated last year
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆213Updated last week
• sanger-pathogens / snp-sites
  Finds SNP sites from a multi-FASTA alignment file
  ☆266Updated 4 years ago
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆319Updated 2 years ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆208Updated 2 years ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆217Updated last year
• nf-core / mag
  Assembly and binning of metagenomes
  ☆249Updated last week
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆249Updated 2 years ago
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆392Updated 4 months ago
• marbl / verkko
  Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…
  ☆365Updated 3 weeks ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆260Updated 2 years ago