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  • REAPR
    [[Category:Software]][[Category:Biology]][[Category:Assembly]] ...n. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.
    3 KB (320 words) - 21:35, 21 August 2022
  • MarginPolish
    ...BAM (ONT reads aligned to the assembly), and it produces a polished FASTA assembly. ...rginPolish serves as a standalone assembly polisher, it is also part of an assembly pipeline which includes an ultrafast nanopore assembler Shasta and a multi-
    3 KB (320 words) - 21:22, 6 December 2019
  • Category:Assembly
    Short Sequence Assembly software.
    20 members (0 subcategories, 0 files) - 15:24, 23 August 2022
  • AMOS
    [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Assembly]] ...and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure. In this sense, AMOS is both a design philosophy and a softw
    3 KB (344 words) - 12:41, 12 August 2022
  • Transrate
    [[Category:Software]][[Category:Biology]][[Category:Assembly]] ...ntigs from an assembly, and help decide when to stop trying to improve the assembly.
    3 KB (316 words) - 16:54, 22 August 2022
  • Haplomerger2
    ...easy-to-use automated pipeline for improving geneome assembly in the post-assembly stage. It consists of a set of executables as well as wrappers for several ...elic relations between haplotype sequences in a highly-polymorphic diploid assembly, and then reconstruct and output two separated haploid sub-assemblies, the
    3 KB (339 words) - 19:05, 12 August 2022
  • Redundans
    Redundans pipeline assists an assembly of heterozygous genomes. ...ddition, Redundans will automatically close the gaps resulting from genome assembly or scaffolding.
    3 KB (332 words) - 21:24, 6 December 2019
  • IAssembler
    [[Category:Software]][[Category:Biology]][[Category:Assembly]] ...y in EST assembly than other existing assemblers by employing an iterative assembly strategy and automated error corrections of mis-assemblies.
    3 KB (301 words) - 18:39, 15 August 2022
  • Aquamis
    AQUAMIS is a pipeline for routine assembly and quality assessment of microbial isolate sequencing experiments. It is b * shovill (based on Spades) for de-novo assembly
    3 KB (348 words) - 22:07, 20 October 2023
  • ABruijn
    ...ts of raw reads. This coarse sequence is then polished into a high quality assembly. ...with 50x coverage takes less than an hour on a modern desktop, while yeast assembly takes about 5 hours. A eukaryotic genome of size 200 Mbp can be assembled w
    3 KB (354 words) - 20:09, 24 August 2022
  • LongStitch
    A genome assembly correction and scaffolding pipeline using long reads, consisting of up to t * Tigmint cuts the draft assembly at potentially misassembled regions
    3 KB (314 words) - 19:00, 10 October 2022
  • Scapp
    [[Category:Software]][[Category:Genomics]][[Category:Assembly]] SCAPP assembles plasmids from metagenomic assembly graphs.
    2 KB (267 words) - 20:57, 10 August 2023
  • PB-Assembly
    |{{#vardefine:app|pb-assembly}} |{{#vardefine:url|https://github.com/PacificBiosciences/pb-assembly}}
    2 KB (269 words) - 20:11, 24 August 2022
  • Minipolish
    Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not inclu Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it
    3 KB (338 words) - 14:53, 9 December 2019
  • GAML
    ...is a prototype genome assembly tool based on maximizing likelihood of the assembly in a model encompaasing error rate, insert length and other features of ind
    2 KB (279 words) - 16:51, 15 August 2022
  • Rascaf
    ...rst computes a set of candidate contig connections from the raw (original) assembly that are supported by the RNA-seq data. Then, in an optional step, the user ...rch/Rascaf/ Song, L., Shankar, D. and Florea, L. "Rascaf: Improving Genome Assembly with RNA-seq Data", The Plant Genome, 2016. doi: 10.3835/plantgenome2016.03
    3 KB (415 words) - 21:30, 21 August 2022
  • Shasta
    Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are th ...128 virtual processors and 1952 GB of memory). The compute cost of such an assembly is around $20 at AWS spot market or reserved prices.
    3 KB (402 words) - 21:24, 6 December 2019
  • Purge haplotigs
    ...are two examples of how Purge Haplotigs can improve a haploid and diploid assembly.
    3 KB (356 words) - 20:27, 12 August 2022
  • Unicycler
    ..., give it both Illumina reads and long reads, and it will conduct a hybrid assembly.
    2 KB (292 words) - 21:29, 6 December 2019
  • Minia
    GATB-Minia-Pipeline is a de novo assembly pipeline for Illumina data. It can assemble genomes and metagenomes. * Minia 3 (contigs assembly) based on the BCALM2 (unitigs assembly) tool
    2 KB (285 words) - 13:31, 15 August 2022

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