Alternatives and similar repositories for minimap2:

Users that are interested in minimap2 are comparing it to the libraries listed below

• lh3 / bwa
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
  ☆1,599Updated 3 weeks ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆748Updated 8 months ago
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,707Updated last week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆708Updated 4 months ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,452Updated 8 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆825Updated 7 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆977Updated last month
• tseemann / prokka
  Rapid prokaryotic genome annotation
  ☆888Updated last year
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,288Updated this week
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆854Updated 2 months ago
• samtools / htslib
  C library for high-throughput sequencing data formats
  ☆845Updated this week
• ablab / spades
  SPAdes Genome Assembler
  ☆813Updated this week
• OpenGene / fastp
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆2,056Updated this week
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆778Updated this week
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆494Updated last year
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆610Updated 2 years ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆813Updated last week
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆674Updated last week
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆820Updated last month
• broadinstitute / gatk
  Official code repository for GATK versions 4 and up
  ☆1,791Updated this week
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆499Updated 5 months ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆751Updated 5 months ago
• nanoporetech / dorado
  Oxford Nanopore's Basecaller
  ☆630Updated 2 weeks ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆801Updated 10 months ago
• shenwei356 / seqkit
  A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  ☆1,385Updated this week
• 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…
  ☆819Updated 3 weeks ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆609Updated 11 months ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆426Updated last year
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆587Updated this week
• bbuchfink / diamond
  Accelerated BLAST compatible local sequence aligner.
  ☆1,127Updated last month