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)
  ☆1,682Updated 8 months ago
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,808Updated 2 weeks ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆798Updated last month
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,515Updated 6 months ago
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆755Updated 2 weeks ago
• ablab / spades
  SPAdes Genome Assembler
  ☆883Updated this week
• OpenGene / fastp
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆2,240Updated 2 weeks ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆695Updated 3 weeks ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆883Updated 7 months ago
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆853Updated 2 weeks ago
• tseemann / prokka
  Rapid prokaryotic genome annotation
  ☆942Updated last year
• nanoporetech / dorado
  Oxford Nanopore's Basecaller
  ☆765Updated 3 weeks ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,397Updated this week
• kblin / ncbi-genome-download
  Scripts to download genomes from the NCBI FTP servers
  ☆1,051Updated 4 months ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆877Updated 10 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆557Updated 2 weeks ago
• ncbi / sra-tools
  SRA Tools
  ☆1,282Updated this week
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆878Updated last week
• samtools / htslib
  C library for high-throughput sequencing data formats
  ☆892Updated last week
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆851Updated last year
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,013Updated 9 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆520Updated 3 months ago
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆654Updated 3 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.
  ☆1,037Updated 3 weeks ago
• shenwei356 / seqkit
  A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  ☆1,489Updated last week
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆819Updated 4 months ago
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆710Updated 8 months ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆856Updated 6 months ago
• bbuchfink / diamond
  Accelerated BLAST compatible local sequence aligner.
  ☆1,215Updated last week
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,163Updated last week