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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
  • 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
  • Necklace
    ...notation. Necklace is a software pipeline to run genome-guided and de novo assembly and combine the resulting transcriptomes with reference genome annotations.
    3 KB (312 words) - 21:22, 6 December 2019
  • HapCUT2
    accuracy. We found that previously described haplotype assembly methods are Edge, P., Bafna, V. & Bansal, V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. gr.213462.116 (2016). doi:
    3 KB (317 words) - 20:03, 8 March 2022
  • Inspector
    Inspector is a tool for assembly evaluation with long read data. The input includes a contig file, long read ...-02527-4 Chen, Y., Zhang, Y., Wang, A.Y. et al. Accurate long-read de novo assembly evaluation with Inspector. Genome Biol 22, 312 (2021).]
    3 KB (319 words) - 18:50, 15 August 2022
  • Consed
    calling, sequence comparisons, and sequence assembly. Phred, Cross_match, ...encing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.
    3 KB (348 words) - 18:39, 12 August 2022
  • SOAPdenovo
    ...enovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble
    2 KB (314 words) - 00:05, 22 August 2022
  • MECAT
    MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alig ...Han, Feng Luo, Zhi Xie. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nature Methods, 2017, 14: 1072-1074]
    3 KB (324 words) - 18:29, 18 August 2022
  • 3d-dna
    ...the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. ...hamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., et al. (2017). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.
    3 KB (328 words) - 17:51, 10 June 2022
  • Ensembl Tools
    * Assembly converter - map (liftover) data's coordinates to the current assembly.
    3 KB (333 words) - 18:52, 12 August 2022
  • Meraculous
    ...ansparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide va
    3 KB (354 words) - 18:36, 10 June 2022
  • Racon
    ...as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step, such as Miniasm. ...which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while provi
    3 KB (364 words) - 21:24, 21 August 2022
  • SEQuel
    ...contain a substantial number of errors that need to be corrected after the assembly process. The algorithm behind SEQuel makes use of a graph structure called
    3 KB (382 words) - 22:39, 21 August 2022
  • Maq
    Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
    3 KB (377 words) - 19:47, 12 August 2022
  • Tigmint
    ...inked reads from 10x Genomics Chromium. The reads are first aligned to the assembly, and the extents of the large DNA molecules are inferred from the alignment ...rg Bohlmann, Steven J.M. Jones and Inanc Birol (2018). Tigmint: correcting assembly errors using linked reads from large molecules. BMC Bioinformatics, 19(1).]
    3 KB (370 words) - 21:29, 6 December 2019
  • VirusDetect
    ...s to the known virus reference database (GenBank gbvrl) as well as de novo assembly using Velvet with automated parameter optimization. The assembled contigs a
    3 KB (377 words) - 23:22, 30 July 2020
  • FALCON
    Falcon: a set of tools for fast aligning long reads for consensus and assembly ...kit is a set of simple code collection which I use for studying efficient assembly algorithm for haploid and diploid genomes. It has some back-end code implem
    3 KB (395 words) - 15:19, 15 August 2022
  • SRAssembler
    ...mbler repository is the distribution point of our code for selective local assembly of genomic regions matching a homologous query protein or DNA sequence. ...Chou, and Volker P. Brendel (2018) SRAssembler: Selective Recursive local Assembly of homologous genomic regions.]
    3 KB (381 words) - 15:33, 27 May 2022
  • MEGAHIT
    ...oil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG c ...HIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, doi: 10.1093/bioinformatics/b
    3 KB (367 words) - 18:31, 18 August 2022
  • GRIDSS
    ...based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence. ...specific genomic rearrangement detection using positional de Bruijn graph assembly. Genome Research, 2017 doi: 10.1101/gr.222109.117]
    3 KB (388 words) - 21:20, 6 December 2019
  • Wengan
    identifies miss-assemblies at different steps of the assembly process. For more information ...., Buena-Atienza, E., Ossowski, S. and Sagot,M-F. Efficient hybrid de novo assembly of human genomes with WENGAN. Nature Biotechnology (2020),
    4 KB (472 words) - 20:55, 12 August 2022
  • PsiCLASS
    ...robust with the aggregation method used, including the built-in voting and assembly-based approaches such as StringTie-merge and TACO. Therefore, it can be eff ...nd Florea, L. A multi-sample approach increases the accuracy of transcript assembly. Nat Commun 10, 5000 (2019)]
    4 KB (480 words) - 15:00, 14 December 2022
  • TACO
    TACO: Multi-sample transcriptome assembly from RNA-Seq
    2 KB (234 words) - 18:53, 1 June 2022
  • RACA
    RACA: Reference-Assisted Chromosome Assembly
    2 KB (235 words) - 19:45, 10 June 2022
  • BUSCO
    BUSCO stands for Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Ortholo BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
    5 KB (607 words) - 19:38, 27 March 2023
  • FRAMA
    Description: a transcriptome assembly and mRNA annotation pipeline
    2 KB (236 words) - 21:21, 6 December 2019
  • Ipyrad
    ipyrad, an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, d
    2 KB (239 words) - 19:00, 15 August 2022
  • MetaBCC-LR
    ...bly helps to enhance the assembly quality while significantly reducing the assembly cost in terms of time and memory usage. The efficiency and accuracy of Meta
    6 KB (774 words) - 14:28, 15 December 2022
  • Assemblytics
    Assemblytics: a web analytics tool for the detection of variants from an assembly
    2 KB (252 words) - 17:02, 29 September 2020
  • Asset
    ...acbio, 10X, Bionano, HiC) to accumulate the support evidence for a de novo assembly.
    2 KB (253 words) - 20:07, 15 June 2023
  • NECAT
    NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.
    2 KB (250 words) - 13:32, 23 June 2020
  • Clview
    Clview is an nteractive tool for inspecting the ACE format assembly files generated by CAP3 or phrap.
    2 KB (252 words) - 13:48, 15 August 2022
  • PurgeDups
    Purge haplotigs and overlaps in an assembly based on read depth
    2 KB (257 words) - 18:50, 27 May 2022
  • Rainbow
    clustering and de novo assembly.
    2 KB (254 words) - 21:24, 6 December 2019
  • Staden
    A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX
    2 KB (254 words) - 15:59, 22 August 2022
  • Skmer
    ...mes from low-coverage sequencing reads (genome-skims), without needing any assembly or alignment step.
    2 KB (260 words) - 13:31, 15 August 2022
  • WhatsHap
    ...ts using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short r
    2 KB (269 words) - 21:29, 6 December 2019
  • JCVI
    ...libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
    2 KB (265 words) - 14:30, 4 September 2020
  • Yagcloser
    [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Assembly]]
    2 KB (265 words) - 19:07, 1 April 2024
  • RagTag
    Fast reference-guided genome assembly scaffolding
    2 KB (263 words) - 15:27, 13 August 2020
  • Pbipa
    ...ved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce h
    2 KB (268 words) - 21:58, 27 April 2022
  • Fast-gep
    ...r high-resolution genealogical relationship of bacterial isolates with WGS assembly data.
    2 KB (283 words) - 15:46, 22 July 2022
  • DRAP
    Short read RNASeq de novo assembly is a well established method to study transcription of organisms lacking a
    2 KB (280 words) - 21:20, 6 December 2019
  • 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 assem
    2 KB (286 words) - 18:13, 23 August 2022
  • FALCON fc run cfg
    # The length cutoff used for seed reads usef for pre-assembly
    2 KB (248 words) - 20:31, 2 August 2021
  • PRICE
    ...es from such complex datasets, and it is also being applied to the de novo assembly of large individual genomes.
    2 KB (286 words) - 16:26, 10 June 2022
  • GROCSVs
    ...eline for identifying large-scale structural variants, performing sequence assembly at the breakpoints, and reconstructing the complex structural variants usin
    2 KB (274 words) - 21:21, 6 December 2019
  • PhyloFlash
    ...KB Seah, Elmar Pruesse. phyloFlash — Rapid SSU rRNA profiling and targeted assembly from metagenomes.]
    2 KB (279 words) - 00:09, 29 October 2020
  • BRIG
    ...arisons between a large number of genomes, with a focus on handling genome assembly data.
    2 KB (278 words) - 16:25, 10 June 2022
  • RaGOO
    A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome.
    2 KB (280 words) - 21:24, 6 December 2019
  • GetOrganelle
    ...Li. 2018. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. bioRxiv, 256479.]
    2 KB (275 words) - 21:21, 6 December 2019
  • FALCON fc large run cfg
    # The length cutoff used for seed reads usef for pre-assembly
    2 KB (266 words) - 20:30, 2 August 2021

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