Alternatives and similar repositories for NextGenMap

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

• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆106Updated 4 years ago
• CSB5 / lofreq
  LoFreq Star: Sensitive variant calling from sequencing data
  ☆105Updated 2 years ago
• parklab / bamsnap
  ☆122Updated 7 months ago
• glennhickey / progressiveCactus
  Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
  ☆85Updated 7 years ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆97Updated last year
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆140Updated 3 weeks ago
• AndersenLab / VCF-kit
  VCF-kit: Assorted utilities for the variant call format
  ☆130Updated last month
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆102Updated 4 years ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆118Updated 2 months ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆108Updated 4 years ago
• COMBINE-lab / RapMap
  Rapid sensitive and accurate read mapping via quasi-mapping
  ☆89Updated 5 years ago
• sujaikumar / assemblage
  Tools for working with second gen assemblies, fasta sequences, etc
  ☆93Updated 8 years ago
• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆72Updated 9 years ago
• compbiocore / VariantVisualization.jl
  Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
  ☆86Updated last year
• dzerbino / oases
  De novo transcriptome assembler for short reads
  ☆62Updated 7 years ago
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆143Updated 8 years ago
• dentearl / mafTools
  Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
  ☆108Updated 3 years ago
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆134Updated 4 years ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆71Updated 3 years ago
• BioInf-Wuerzburg / proovread
  PacBio hybrid error correction through iterative short read consensus
  ☆61Updated 6 years ago
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated last month
• mroosmalen / nanosv
  SV caller for nanopore data
  ☆91Updated 5 years ago
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• nhansen / SVanalyzer
  Tools for the analysis of structural variation in genomes
  ☆79Updated last year
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆100Updated 3 weeks ago
• statgen / bamUtil
  ☆91Updated 3 years ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆185Updated last year
• nanoporetech / ont-assembly-polish
  ONT assembly and Illumina polishing pipeline
  ☆89Updated 4 years ago