Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most co...1290 days ago
CoverM: Read coverage calculator for metagenomics
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator foc...rm contig (help). Calculating coverage by read mapping, its input can either be BAM files sorted by reference, or raw reads and...1163 days ago
312 days ago
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/61467721210 days ago
IVA: accurate de novo assembly of RNA virus genomes
IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples fro...1109 days ago
LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits...n approach that has been successful with short reads. ht...1109 days ago
k-mers tutorial - classification and taxonomy
DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking...hough that has become an ahem area of interest recently, if you read into...1045 days ago
RagTag: a collection of software tools for scaffolding and improving modern genome assemblies
RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: Homology-based misassembly correction Homology-based assembly scaffolding and patching Scaffold merging1029 days ago
938 days ago
Peregrine & SHIMMER Genome Assembly Toolkit
Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from rea...arse HIereachical MimiMizER (SHIMMER) for fast read-to-re...933 days ago