RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Scha...takes ~2 minutes. Intact ordering and orienting of contigs. Chimeric contig correction GFF lift-over Structural va...1904 days ago
FLAS: fast and high throughput algorithm for PacBio long read self-correction.
FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes misalignments for accuracy.1838 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simu...single, paired-end, or mate-pair Illumina reads, as...1805 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide...package represents a complete pipeline: it takes raw PB / ONT reads as i...1825 days ago
LRSDAY: Long-read Sequencing Data Analysis for Yeasts
Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in r...accharomyces cerevisiae, has many isolates currently being sequenced with long reads.&nbs...1773 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Scha...ling takes ~2 minutes. Intact ordering and orienting of contigs. Misassembly correction GFF lift-over Structural va...1712 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
Miniasm is a great long-read assembly tool: straight-forward, effec...e of stitched-together pieces of long reads. Racon is a great poli...so very fast and well suited for long-read data. However, it operates on...lishing a miniasm assembly: Adding read depth...1675 days ago
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ngs-bits - Short-read sequencing tools
Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for Windows1630 days ago