Alternatives and similar repositories for khmer:

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

• cyverse / atmosphere
  Where cloud lives.
  ☆332Updated 2 years ago
• ropensci-archive / rplos
  ARCHIVED R client for the PLoS Journals API
  ☆314Updated 2 years ago
• broadinstitute / picard
  A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
  ☆994Updated this week
• chapmanb / bcbb
  Incubator for useful bioinformatics code, primarily in Python and R
  ☆614Updated last week
• google / nucleus
  Python and C++ code for reading and writing genomics data.
  ☆787Updated 3 years ago
• dzerbino / velvet
  Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo sh…
  ☆285Updated 6 years ago
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆658Updated this week
• psas / av3-fc
  Event driven flight computer for rockets. Flown on L-10 and L-11.
  ☆426Updated 7 years ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆491Updated this week
• broadgsa / gatk
  Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk…
  ☆295Updated 6 years ago
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆467Updated this week
• sourmash-bio / sourmash
  Quickly search, compare, and analyze genomic and metagenomic data sets.
  ☆486Updated this week
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆670Updated this week
• GMOD / jbrowse
  JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
  ☆466Updated last week
• scikit-bio / scikit-bio
  scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resourc…
  ☆908Updated 3 weeks ago
• pysam-developers / pysam
  Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…
  ☆806Updated this week
• bcbio / bcbio-nextgen
  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
  ☆996Updated 5 months ago
• tiagoantao / bioinf-python
  Python for Bioinformatics
  ☆250Updated 4 years ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆802Updated 8 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆958Updated last month
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆580Updated last month
• tskit-dev / msprime
  Simulate genealogical trees and genomic sequence data using population genetic models
  ☆185Updated 2 weeks ago
• lh3 / bioawk
  BWK awk modified for biological data
  ☆602Updated 2 years ago
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆603Updated 2 years ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆423Updated 7 months ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,267Updated last week
• samtools / htslib
  C library for high-throughput sequencing data formats
  ☆829Updated this week
• jtleek / genomicspapers
  The Leek group guide to genomics papers
  ☆481Updated 6 years ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,428Updated 6 months ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆788Updated 8 months ago