Alternatives and similar repositories for mafTools

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

• TNTurnerLab / HAT
  HAT is a set of tools for calling de novo variants from whole-genome sequencing data.
  ☆24Updated last year
• ktan8 / nanopore_telomere_basecall
  ☆14Updated 2 years ago
• sinamajidian / phaseme
  A tool set to assess the quality of the per read phasing and reduce the errors.
  ☆12Updated 5 years ago
• CMU-SAFARI / FastRemap
  FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: http…
  ☆26Updated 3 years ago
• bio-ontology-research-group / DeepSVP
  Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity
  ☆16Updated 3 years ago
• schneebergerlab / GameteBinning
  ☆12Updated 4 years ago
• DecodeGenetics / LRcaller
  ☆16Updated 3 years ago
• alshai / rowbowt
  run-length BWT tools for genomic sequences
  ☆19Updated 3 years ago
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆24Updated last year
• RitchieLabIGH / iMOKA
  interactive Multi Objective K-mer Analysis
  ☆23Updated 2 years ago
• Gaius-Augustus / clamsa
  ClaMSA (Classify Multiple Sequence Alignments).
  ☆13Updated 9 months ago
• bahlolab / superSTR
  A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.
  ☆18Updated last week
• mchaisso / mcutils
  ☆12Updated last week
• ChaissonLab / hmcnc
  Hidden Markov Model based Copy number caller
  ☆20Updated 10 months ago
• XuepengSun / apple_diploid_genomes
  ☆10Updated 5 years ago
• Gabaldonlab / haplotypo
  This is the Haplotypo repository
  ☆20Updated last year
• aganezov / RCK
  RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes
  ☆17Updated 5 years ago
• wjidea / defusion
  defusion
  ☆14Updated 4 years ago
• luntergroup / bamsplit
  Split a BAM file by haplotype support
  ☆16Updated 7 years ago
• marschall-lab / strand-seq-graph-phasing
  ☆12Updated 3 months ago
• bioinfo-ut / GeneToCN
  Gene copy number prediction from k-mer frequencies
  ☆13Updated last year
• splicebox / PsiCLASS
  Simultaneous multi-sample transcript assembler for RNA-seq data
  ☆17Updated 9 months ago
• luntergroup / polyploid
  Benchmarking variant calling in polyploids
  ☆15Updated 3 years ago
• yuansliu / minirmd
  ☆12Updated 2 years ago
• DaehwanKimLab / seqwho
  SeqWho - A reliable and rapid FASTQ(A) file classifier
  ☆10Updated 3 years ago
• gjun / muCNV
  ☆20Updated last year
• jmonlong / sveval
  Functions to compare a SV call sets against a truth set.
  ☆30Updated 3 months ago
• jfoox / abrfngs2
  Analysis and figure generation code for the ABRF NGS Phase II Study on DNA-seq reproducibility
  ☆19Updated 4 years ago
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 3 years ago
• clemgoub / TypeTE
  Genotyping of segregating mobile elements insertions
  ☆19Updated 4 years ago