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)
  ☆1,633Updated 3 months ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆766Updated 2 weeks ago
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,745Updated this week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆724Updated 7 months ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,476Updated last month
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆850Updated 2 months ago
• ablab / spades
  SPAdes Genome Assembler
  ☆852Updated last week
• OpenGene / fastp
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆2,121Updated last week
• nanoporetech / dorado
  Oxford Nanopore's Basecaller
  ☆690Updated last month
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆865Updated 5 months ago
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆809Updated last week
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆683Updated this week
• ncbi / sra-tools
  SRA Tools
  ☆1,235Updated this week
• kblin / ncbi-genome-download
  Scripts to download genomes from the NCBI FTP servers
  ☆1,021Updated 11 months ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,327Updated last week
• samtools / htslib
  C library for high-throughput sequencing data formats
  ☆860Updated this week
• tseemann / prokka
  Rapid prokaryotic genome annotation
  ☆913Updated last year
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆985Updated 4 months ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆835Updated 2 weeks ago
• shenwei356 / seqkit
  A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  ☆1,439Updated this week
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆517Updated last year
• 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…
  ☆836Updated last month
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,063Updated last week
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆656Updated 3 months ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆813Updated last year
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆834Updated last month
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆621Updated 2 years ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆783Updated this week
• samtools / bcftools
  This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…
  ☆781Updated 2 weeks ago
• bbuchfink / diamond
  Accelerated BLAST compatible local sequence aligner.
  ☆1,163Updated 3 weeks ago