Alternatives and similar repositories for simNGS:

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

• mikolmogorov / pbclip
  A simple tool to fix PacBio fasta/q that was not properly split into subreads
  ☆15Updated 3 years ago
• lh3 / sdust
  Symmetric DUST for finding low-complexity regions in DNA sequences
  ☆37Updated last year
• EvolBioInf / fur
  Find Unique genomic Regions
  ☆29Updated 3 weeks ago
• VGP / vgp-tools
  ☆28Updated 2 weeks ago
• kdm9 / axe
  Rapid competitive read demulitplexer. Made with tries.
  ☆23Updated last year
• adigenova / fast-sg
  Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.
  ☆22Updated 6 years ago
• PacificBiosciences / svpack
  Structural variant (SV) analysis tools
  ☆36Updated 9 months ago
• Gabaldonlab / jloh
  A tool to extract LOH blocks from VCF, BAM and FASTA data
  ☆21Updated 7 months ago
• myriad-opensource / samwell
  Samwell: a python package for using genomic files... well
  ☆20Updated 2 years ago
• lh3 / gfa1
  This repo is deprecated. Please use gfatools instead.
  ☆16Updated 6 years ago
• douglasgscofield / PacBio-utilities
  Collection of utilities for working with PacBio-based assemblies
  ☆13Updated 2 years ago
• rcedgar / urmap
  URMAP ultra-fast read mapper
  ☆38Updated 4 years ago
• jts / mbtools
  ☆14Updated last year
• edawson / svaha
  Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]
  ☆12Updated last year
• richarddurbin / modimizer
  a toolset for fast DNA read set matching and assembly using a new type of reduced kmer
  ☆37Updated 3 years ago
• kamimrcht / REINDEER
  REINDEER REad Index for abuNDancE quERy
  ☆57Updated 9 months ago
• cdarby / samovar
  Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters
  ☆24Updated 6 years ago
• karel-brinda / samsift
  SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.
  ☆23Updated 7 years ago
• annalam / seqkit
  Toolkit for manipulating FASTA and SAM files
  ☆18Updated last year
• lbcb-sci / ra
  Assembler for raw de novo genome assembly of long uncorrected reads.
  ☆37Updated 5 years ago
• pierrepeterlongo / kmer2sequences
  Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.
  ☆21Updated last year
• quinlan-lab / pathoscore
  pathoscore evaluates variant pathogenicity tools and scores.
  ☆21Updated 3 years ago
• iqbal-lab-org / minos
  Variant call adjudication
  ☆16Updated 10 months ago
• jts / bri
  Bam Read Index - Extract alignments from a bam file by readname
  ☆25Updated last year
• atifrahman / HAWK
  Hitting associations with k-mers
  ☆45Updated 2 years ago
• cpockrandt / PhyloCSFpp
  PhyloCSF++ computes PhyloCSF tracks for whole-genome multiple sequence alignments, scores single MSA, annotates CDS features in GFF/GTF f…
  ☆31Updated 3 years ago
• NDBL / HECIL
  Hybrid Error Correction of Long Reads using Iterative Learning
  ☆10Updated 6 years ago
• karel-brinda / ococo
  Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
  ☆47Updated 6 years ago
• shendurelab / MetaPhase
  The software involved in the MetaPhase project, as described in G3 (http://dx.doi.org/10.1534/g3.114.011825)
  ☆17Updated 6 years ago
• edawson / rkmh
  Classify sequencing reads using MinHash.
  ☆48Updated 5 years ago