Alternatives and similar repositories for GenomeAlignmentTools

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

• phasegenomics / juicebox_scripts
  A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats
  ☆68Updated 4 years ago
• mapleforest / HaploMerger2
  ☆44Updated 8 years ago
• mahulchak / svmu
  A program to call variants from genome alignment
  ☆81Updated 4 months ago
• shilpagarg / DipAsm
  ☆77Updated 5 years ago
• JanaSperschneider / FindTelomeres
  A python script for finding telomeric repeats (TTAGGG/CCCTAA) in FASTA files
  ☆34Updated 3 years ago
• zeeev / smartie-sv
  calling SVs from Blasr contig level alignments
  ☆54Updated 7 years ago
• clemgoub / dnaPipeTE
  dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…
  ☆58Updated 2 years ago
• 0xTCG / biser
  A fast tool for detecting and decomposing segmental duplications in genome assemblies
  ☆50Updated last month
• aubombarely / Organelle_PBA
  A software to assemble chloroplast and mitochodrial genomes using PacBio data
  ☆40Updated 5 years ago
• CAFS-bioinformatics / LR_Gapcloser
  use long sequenced reads to close gaps in assemblies
  ☆39Updated 7 years ago
• simon19891216 / CentIER
  ☆37Updated last month
• sjteresi / TE_Density
  Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com…
  ☆34Updated 11 months ago
• LiLabAtVT / DeepTE
  Neural network classification of TE
  ☆95Updated 3 months ago
• liangclab / HERA
  ☆77Updated 5 years ago
• josephryan / estimate_genome_size.pl
  Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
  ☆57Updated 2 years ago
• TF-Chan-Lab / panGraphViewer
  Show pangenome graphs in an easy way
  ☆56Updated last month
• ArimaGenomics / mapping_pipeline
  Mapping pipeline for data generated using Arima-HiC
  ☆80Updated last year
• baozg / assembly-annotation-pipeline
  Plant genome assembly and annotation pipeline using snakemake
  ☆47Updated 4 months ago
• phyloacc / PhyloAcc
  PhyloAcc a software to detect the changes of conservation of a genomic region
  ☆32Updated 5 months ago
• tanghaibao / allhic
  Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
  ☆60Updated 8 months ago
• JiangYuLab / CNVcaller
  ☆42Updated last year
• Gaius-Augustus / TSEBRA
  TSEBRA: Transcript Selector for BRAKER
  ☆48Updated 10 months ago
• kakitone / finishingTool
  finshingTool
  ☆54Updated 8 years ago
• oushujun / LTR_FINDER_parallel
  A parallel wrapper for LTR_FINDER
  ☆54Updated 5 months ago
• PacificBiosciences / jasmine
  Call select base modifications in PacBio HiFi reads
  ☆14Updated 7 months ago
• wangyibin / CPhasing
  C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.
  ☆57Updated 2 months ago
• phasegenomics / hic_qc
  A (very) simple script to QC Hi-C data.
  ☆26Updated 9 months ago
• shingocat / lrscaf
  TGS scaffolding
  ☆46Updated 3 years ago
• hillerlab / make_lastz_chains
  Portable solution to generate genome alignment chains using lastz
  ☆58Updated 3 months ago
• c-zhou / oatk
  A organelle de novo genome assembly toolkit
  ☆69Updated 6 months ago