Tool Library list page for genomics topic with tag 'Sequence assembly'



6 tools

Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.

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Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.

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Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

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Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.

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St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.

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A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.

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