Peregrine & SHIMMER Genome Assembly Toolkit
Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 9...to polished consensus. It uses Sparse HIereachical MimiMizER (SHIMMER) for fast read-to-read overlaping witho...885 days ago
UniqueKmer: Generate unique KMERs for every contig in a FASTA file
Generate unique k-mers for every contig in a FASTA file. Unique k-mer is consiste...rse strands). This tool accepts the input of a FASTA file consisting of many cont...ique k-mer file and Genome file can be used for fastv: https://github.com/Ope...884 days ago
836 days ago
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffA...Bowtie2, but much more quickly. While exhibiting similar speed to the ultrafast STAR aligner, PuffAligner req...759 days ago
gfastats: The swiss army knife for genome assembly.
gfastats is a single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation. gfastats also allows seamless...619 days ago
HairSplitter: assembling long reads in an unknown number of haplotypes
Pros and cons of HairSplitter Limitations of HairSplitter: Not very fast: it re-polishes the whole assembly Limited in the number of haplotypes Strengths of HairSplitter: V...529 days ago
408 days ago
OMArk: software for proteome (protein-coding gene repertoire) quality assessment
...tion from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins int...87 days ago
UniAligner: a parameter-free framework for fast sequence alignment
UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatic...71 days ago
Alvis: a tool for contig and read ALignment VISualisation and chimera detection
Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety...11 days ago