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  • Short Sequence Assembly software.
    3 members (0 subcategories, 0 files) - 20:43, 21 September 2012
  • ...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
  • 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
  • ...n. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls. ...://www.genomebiology.com/2013/14/5/R47/ REAPR: a universal tool for genome assembly evaluation. Genome Biology 2013, 14:R47, doi:10.1186/gb-2013-14-5-r47.]
    3 KB (318 words) - 21:24, 6 December 2019
  • ...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 (339 words) - 21:01, 6 December 2019
  • ...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 (352 words) - 21:11, 6 December 2019
  • ...ntigs from an assembly, and help decide when to stop trying to improve the assembly.
    3 KB (314 words) - 21:29, 6 December 2019
  • |{{#vardefine:app|pb-assembly}} |{{#vardefine:url|https://github.com/PacificBiosciences/pb-assembly}}
    2 KB (265 words) - 21:22, 6 December 2019
  • 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
  • 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
  • ..., give it both Illumina reads and long reads, and it will conduct a hybrid assembly.
    2 KB (292 words) - 21:29, 6 December 2019
  • DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, R ...er design as an objective function. In addition, for each contig within an assembly, RSEM-EVAL provides a score that assesses how well that contig is supported
    4 KB (476 words) - 21:20, 6 December 2019
  • ...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) - 21:20, 6 December 2019
  • Assembly Likelihood Estimator ALE is a probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. It allows for the rapid dis
    2 KB (285 words) - 21:11, 6 December 2019
  • ...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 (416 words) - 21:24, 6 December 2019
  • ...rmation is constructed with the compressed reads to enable the final-stage assembly. DBG2OLC: Efficient Assembly of Large Genomes Using the Compressed Overlap Graph. Chengxi Ye, Chris Hill
    3 KB (429 words) - 21:20, 6 December 2019
  • ...y in EST assembly than other existing assemblers by employing an iterative assembly strategy and automated error corrections of mis-assemblies. ...53 Zheng Y, Zhao L, Gao J, Fei Z. (2011) iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics 12:453]
    3 KB (299 words) - 21:21, 6 December 2019
  • ...ulti-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3
    2 KB (320 words) - 21:29, 6 December 2019
  • ...ast sequence, Fast-Plast identifies chloroplast genes present in the final assembly. .... A coverage analysis is then conducted to assess the quality of the final assembly.
    4 KB (487 words) - 21:20, 6 December 2019
  • ...ulti-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3
    3 KB (342 words) - 21:29, 6 December 2019

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