Alternatives and similar repositories for velvet

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

• jts / sga
  de novo sequence assembler using string graphs
  ☆240Updated 5 years ago
• lh3 / miniasm
  Ultrafast de novo assembly for long noisy reads (though having no consensus step)
  ☆321Updated last year
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆232Updated 4 years ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆424Updated 3 weeks ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆363Updated 3 years ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆291Updated 8 months ago
• mummer4 / mummer
  Mummer alignment tool
  ☆510Updated 4 months ago
• refresh-bio / KMC
  Fast and frugal disk based k-mer counter
  ☆294Updated 6 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆510Updated last year
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆470Updated last month
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆338Updated this week
• gmarcais / Jellyfish
  A fast multi-threaded k-mer counter
  ☆501Updated last year
• aquaskyline / SOAPdenovo2
  Next generation sequencing reads de novo assembler.
  ☆232Updated last year
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆594Updated last month
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆441Updated 3 weeks ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆316Updated 2 years ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆318Updated last week
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆371Updated 9 months ago
• ablab / quast
  Genome assembly evaluation tool
  ☆440Updated 6 months ago
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆310Updated 3 months ago
• najoshi / sickle
  Windowed Adaptive Trimming for fastq files using quality
  ☆220Updated 8 years ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆260Updated 7 months ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆212Updated last year
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆632Updated 2 months ago
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆299Updated last year
• pcingola / SnpEff
  ☆277Updated 3 months ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆369Updated 3 years ago
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆409Updated 4 months ago
• usadellab / Trimmomatic
  ☆251Updated last year
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆327Updated 3 years ago