Alternatives and similar repositories for RapMap

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

• relipmoc / skewer
  ☆95Updated 2 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆79Updated last year
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago
• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆72Updated 9 years ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆143Updated this week
• walaj / SeqLib
  C++ htslib/bwa-mem/fermi interface for interrogating sequence data
  ☆138Updated last month
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆106Updated 4 years ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆97Updated last year
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆67Updated 4 years ago
• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆88Updated 10 months ago
• lh3 / bgt
  Flexible genotype query among 30,000+ samples whole-genome
  ☆95Updated 5 years ago
• Cibiv / NextGenMap
  NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms whil…
  ☆87Updated 6 years ago
• lh3 / fermi-lite
  Standalone C library for assembling Illumina short reads in small regions
  ☆72Updated 2 years ago
• Kingsford-Group / scallop
  Scallop is a reference-based transcriptome assembler for RNA-seq
  ☆92Updated 4 years ago
• ssadedin / bazam
  A read extraction and realignment tool for next generation sequencing data
  ☆103Updated 2 years ago
• brentp / jigv
  igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
  ☆128Updated 2 years ago
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 4 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆108Updated 4 years ago
• bcgsc / biobloom
  Create Bloom filters for a given reference and then use it to categorize sequences
  ☆76Updated 9 months ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 9 months ago
• dpryan79 / libBigWig
  A C library for handling bigWig files
  ☆81Updated 7 months ago
• gt1 / biobambam2
  Tools for early stage alignment file processing
  ☆95Updated 6 years ago
• lh3 / tabtk
  Toolkit for processing TAB-delimited format
  ☆62Updated 10 months ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 6 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆122Updated 3 months ago
• svviz / svviz
  Read visualizer for structural variants
  ☆84Updated 7 years ago