Search results

Jump to navigation Jump to search

Page title matches

Page text matches

  • 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
  • Ragout
    ...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) - 21:29, 21 August 2022
  • Fast-Plast
    ...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
  • TGICL
    ...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
  • AAFTF
    [[Category:Software]][[Category:Biology]][[Category:Pipeline]][[Category:Assembly]] Automatic Assembly For The Fungi
    2 KB (245 words) - 20:45, 11 August 2022
  • Hapdup
    ...is a pipeline to convert a haploid long read assembly into a dual diploid assembly. The reconstructed haplotypes preserve heterozygous structural variants (in Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using Repeat Graphs", Nature Biotechnology, 2019
    3 KB (324 words) - 21:07, 7 April 2022
  • Hapsembler
    [[Category:Software]][[Category:Biology]][[Category:Assembly]] Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types
    3 KB (332 words) - 18:15, 15 August 2022
  • LIGR
    [[Category:Software]][[Category:Biology]][[Category:Assembly]] LIGR Assembler is a sequence assembly program. It was derived from TIGR Assembler and addresses some of TIGR Asse
    2 KB (249 words) - 19:55, 15 August 2022
  • Evigene
    ...ftware, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate an
    3 KB (372 words) - 21:21, 6 December 2019
  • Trans-ABySS
    De novo assembly of RNAseq data using ABySS ...th/journal/v7/n11/full/nmeth.1517.html Robertson, G., et al. 2010. De novo assembly and analysis of RNA-seq data. Nature Methods 7, 909-912(2010)]
    2 KB (260 words) - 15:39, 10 June 2022
  • ATRAM
    ..., DI Huang, QC Cronk, KP Johnson. 2015\. aTRAM automated target restricted assembly method a fast method for assembling loci across divergent taxa from next-ge aTRAM does targeted ''de novo'' assembly of loci from paired-end Illumina runs and consists of the following tools:
    3 KB (350 words) - 15:23, 12 August 2022
  • Xander
    ...ruijn graphs and protein HMMs. The inclusion of HMM information guides the assembly, with concomitant gene annotation. .... Xander: Employing a Novel Method for Efficient Gene-Targeted Metagenomic Assembly. Microbiome.2015, 3:32. DOI: 10.1186/s40168-015-0093-6.]
    3 KB (381 words) - 19:07, 10 June 2022
  • Zorro
    ...3Mb to 100Mb. The main feature of Zorro is the treatment before and after assembly to avoid errors.
    2 KB (284 words) - 17:54, 22 August 2022
  • FALCON unzip
    ...icBiosciences/FALCON/wiki/FALCON-FALCON-Unzip-%22For-Phased-Diploid-Genome-Assembly-with-Single-Molecule-Real-Time-Sequencing%22
    3 KB (302 words) - 18:53, 12 August 2022
  • FastPlast
    ...ast sequence, Fast-Plast identifies chloroplast genes present in the final assembly.
    2 KB (288 words) - 20:23, 23 May 2022
  • Triobinning
    Programs implementing the trio-binning genome assembly method Koren et al. (2018). "Complete assembly of parental haplotypes with trio binning." Nature Biotechnology 2018/10/22/
    2 KB (276 words) - 13:31, 15 August 2022
  • Newbler
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]][[Category:De Novo]] Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the
    2 KB (305 words) - 16:17, 19 August 2022
  • Assembly-stats
    |{{#vardefine:app|assembly-stats}} |{{#vardefine:url|https://github.com/sanger-pathogens/assembly-stats}}
    2 KB (293 words) - 14:56, 12 August 2022
  • Clover
    [[Category:Assembly]] k-mers.Clover achieves a superior assembly quality in terms of corrected
    2 KB (296 words) - 13:47, 15 August 2022
  • DEXTRACTOR
    assembly and reconstruction from the source .bax.h5 HDF5 files produced by the PacBi to produce a highly accurate consensus sequence as the last step in the assembly
    3 KB (441 words) - 19:20, 10 June 2022
  • HAPCUT
    [[Category:Software]][[Category:Biology]][[Category:Assembly]] HapCUT is a max-cut based algorithm for haplotype assembly that uses the mix of sequenced fragments from the two chromosomes of an ind
    2 KB (298 words) - 18:13, 15 August 2022
  • Platypus
    ...Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole ...um, Andrew O. M. Wilkie, Gil McVean, Gerton Lunter. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing
    3 KB (435 words) - 19:21, 10 June 2022
  • ARC
    ...and a set of semi-similar reference targets is available to initialize the assembly process.
    3 KB (430 words) - 14:32, 12 August 2022
  • Merqury
    Often, genome assembly projects have illumina whole genome sequencing reads available for the asse The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a se
    3 KB (306 words) - 13:54, 12 August 2020
  • Stringtie
    ...lgorithmic techniques from de novo genome assembly to help with transcript assembly. Its input can include not only the spliced read alignments used by referen
    3 KB (301 words) - 20:45, 12 August 2022
  • Oases
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]] the absence of any genomic assembly. It was developed by Marcel Schulz (MPI
    2 KB (293 words) - 17:25, 19 August 2022
  • CAP3
    [[Category:Software]][[Category:Biology]][[Category:Assembly]] CAP3 is a sequence assembly program.
    2 KB (302 words) - 13:19, 15 August 2022
  • Flye
    ...nce. The package also includes a polisher module, which produces the final assembly of high nucleotide-level quality.
    3 KB (317 words) - 21:20, 6 December 2019
  • Quickmerge
    ...For more details, please see the paper that describes it. Citation for ONP assembly merging coming soon!
    3 KB (325 words) - 21:24, 6 December 2019
  • Captus
    ...ation Sequencing) data. Captus was initially designed specifically for the assembly of target-enriched (e.g. via hybridization of RNA or DNA probes) sequencing
    3 KB (321 words) - 16:36, 16 November 2022
  • HLAminer
    ...geted assembly of short sequence reads (HPTASR), performs targeted de novo assembly of HLA NGS reads and align the resulting contigs to reference HLA alleles f ...d, the read is recruited as a candidate for de novo assembly. Upon de novo assembly of all recruited reads, a set of contigs is generated. Only sequence contig
    4 KB (541 words) - 14:55, 14 December 2022

View (previous 50 | next 50) (20 | 50 | 100 | 250 | 500)

Retrieved from "https://help.rc.ufl.edu/doc/Special:Search"