Stars
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Accelerated BLAST compatible local sequence aligner.
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
RAxML Next Generation: faster, easier-to-use and more flexible
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
Toolset for SV simulation, comparison and filtering
Strelka2 germline and somatic small variant caller
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which wil…
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
Structural variation and indel detection by local assembly
De novo genome assembler for long uncorrected reads
A gap-closing software tool that uses long reads to enhance genome assembly.
The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
Kraken taxonomic sequence classification system
Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
base-accurate DNA sequence alignments using WFA and mashmap3
Fast alignment and preprocessing of chromatin profiles
Population-scale genotyping using pangenome graphs