Alternatives and similar repositories for tomahawk:

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

• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆65Updated 2 years ago
• bioinformatics-centre / BayesTyper
  A method for variant graph genotyping based on exact alignment of k-mers
  ☆87Updated 5 years ago
• ekg / bamaddrg
  adds sample names and read-group (RG) tags to BAM alignments
  ☆52Updated 4 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
• grocsvs / grocsvs
  Genome-wide reconstruction of complex structural variants
  ☆39Updated 2 years ago
• Oshlack / STRetch
  Method for detecting STR expansions from short-read sequencing data
  ☆62Updated 3 years ago
• sestaton / Transposome
  A toolkit for annotation of transposable element families from unassembled sequence reads
  ☆30Updated last year
• kehrlab / PopDel
  Population-wide Deletion Calling
  ☆35Updated 6 months ago
• selfdecode / rd-imputation-accuracy
  Phasing and genotype Imputation comparison. Have been evaluated: BEAGLE 5.4, EAGLE 2.4.1, SHAPEIT 4, MINIMAC 4, IMPUTE 5, using accuracy …
  ☆22Updated last year
• bioinform / metasv
  MetaSV: An accurate and integrative structural-variant caller for next generation sequencing
  ☆55Updated 7 years ago
• conchoecia / pauvre
  Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.
  ☆53Updated 4 months ago
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆51Updated 5 years ago
• Illumina / gvcfgenotyper
  A utility for merging and genotyping Illumina-style GVCFs.
  ☆33Updated 6 years ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆95Updated 11 months ago
• lh3 / sdust
  Symmetric DUST for finding low-complexity regions in DNA sequences
  ☆36Updated last year
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆56Updated 3 years ago
• phasegenomics / FALCON-Phase
  FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds
  ☆74Updated 4 years ago
• sequencing / NxTrim
  Adapter trimming and virtual library creation for Illumina Nextera Mate Pair libraries.
  ☆54Updated 6 years ago
• NBISweden / pipelines-nextflow
  A set of workflows written in Nextflow for Genome Annotation.
  ☆45Updated 8 months ago
• lh3 / etrf
  Exact Tandem Repeat Finder (not a TRF replacement)
  ☆48Updated 5 years ago
• lh3 / htsbox
  My experimental tools on top of htslib. NOT OFFICIAL!!!
  ☆55Updated last year
• ekg / fastahack
  utilities for indexing and sequence extraction from FASTA files
  ☆59Updated 3 years ago
• alshai / levioSAM
  Lift-over alignments from variant-aware references
  ☆34Updated 2 years ago
• PacificBiosciences / svpack
  Structural variant (SV) analysis tools
  ☆35Updated 8 months ago
• arq5x / grabix
  a wee tool for random access into BGZF files.
  ☆84Updated 6 years ago
• ydLiu-HIT / deSALT
  deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
  ☆43Updated 2 years ago
• atifrahman / HAWK
  Hitting associations with k-mers
  ☆45Updated 2 years ago
• aquaskyline / LRSIM
  10x Genomics Reads Simulator
  ☆45Updated last year
• zeeev / mergeSVcallers
  heuristics to merge structural variant calls in VCF format.
  ☆36Updated 8 years ago
• tommyau / bamclipper
  Remove primer sequence from BAM alignments by soft-clipping
  ☆31Updated 5 years ago