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  • Short Sequence Assembly software.
    5 members (0 subcategories, 0 files) - 20:57, 12 August 2022
  • ...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: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
  • ...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
  • ...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 (320 words) - 17:24, 10 June 2022
  • 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
  • ...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 (356 words) - 20:43, 11 August 2022
  • ...ntigs from an assembly, and help decide when to stop trying to improve the assembly.
    3 KB (316 words) - 17:17, 10 June 2022
  • 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) - 21:33, 8 August 2022
  • |{{#vardefine:app|pb-assembly}} |{{#vardefine:url|https://github.com/PacificBiosciences/pb-assembly}}
    2 KB (265 words) - 21:22, 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) - 18:56, 12 August 2022
  • 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
  • ...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 (417 words) - 19:14, 10 June 2022
  • ...are two examples of how Purge Haplotigs can improve a haploid and diploid assembly.
    3 KB (356 words) - 20:27, 12 August 2022
  • ..., give it both Illumina reads and long reads, and it will conduct a hybrid assembly.
    2 KB (292 words) - 21:29, 6 December 2019
  • 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) - 17:50, 6 June 2022
  • ...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 (301 words) - 19:05, 12 August 2022
  • ...ple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds). ...orts both small and large genomes (of mammalian scale and complexity). The assembly of highly polymorphic genomes is currently limited.
    3 KB (318 words) - 04:21, 19 February 2022
  • ...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 (340 words) - 20:47, 12 August 2022

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