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• WGS Assembler
  |{{#vardefine:url|http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page}} ...nomics starting in 1999. It was released to SourceForge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was
  3 KB (359 words) - 20:56, 12 August 2022

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• LIGR
  |{{#vardefine:url|http://sourceforge.net/projects/ligr-assembler/}} ...bly program. It was derived from TIGR Assembler and addresses some of TIGR Assembler's shortcomings.
  2 KB (249 words) - 19:55, 15 August 2022
• WGS Assembler
  |{{#vardefine:url|http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page}} ...nomics starting in 1999. It was released to SourceForge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was
  3 KB (359 words) - 20:56, 12 August 2022
• Wgs
  |{{#vardefine:url|http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Paget}} ...nomics starting in 1999. It was released to SourceForge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was
  3 KB (375 words) - 20:55, 12 August 2022
• SOAPdenovo-Trans
  ...alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-len
  2 KB (283 words) - 00:05, 22 August 2022
• PsiCLASS
  ...sets in an experiment. PsiCLASS is both a transcript assembler and a meta-assembler, producing separate transcript sets for the individual samples and a unifie ...efore, it can be effectively used as a multi-sample and as a single-sample assembler, as well as in conventional assemble-and-merge protocols.
  4 KB (480 words) - 15:00, 14 December 2022
• YASM
  ...censed assembler that is designed from the ground up to allow for multiple assembler syntaxes to be supported (e.g. NASM, GNU AS, etc.) in addition to multiple
  2 KB (292 words) - 17:53, 22 August 2022
• Stringtie
  ...into potential transcripts. It is primarily a genome-guided transcriptome assembler, although it can borrow algorithmic techniques from de novo genome assembly
  3 KB (301 words) - 20:45, 12 August 2022
• IDBA-MT
  ...De Novo short read assembler for meta-transcriptome. It is purely de novo assembler based on paired-end RNA sequencing reads only. IDBA-MT is a post-processing
  3 KB (315 words) - 21:21, 6 December 2019
• MetaVelvet
  Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa o MetaVelvet is a single-genome and de Bruijn-graph based assembler Velvet modified and extended for de novo metagenome assembly. The fundament
  3 KB (326 words) - 19:28, 18 August 2022
• Platanus
  |{{#vardefine:url|http://platanus.bio.titech.ac.jp/platanus-assembler}} Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of
  3 KB (318 words) - 21:23, 6 December 2019
• Meraculous
  ...Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of Illumina sequence by eschewing an
  3 KB (354 words) - 18:36, 10 June 2022
• KisSplice
  ...is around 5Gb for 100M reads. KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, no
  3 KB (359 words) - 19:33, 15 August 2022
• Shasta
  The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads Computational methods used by the Shasta assembler include:
  3 KB (402 words) - 21:24, 6 December 2019
• Velvet
  Sequence assembler for very short reads. Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa o
  4 KB (523 words) - 17:06, 14 December 2022
• Pandaseq
  PANDASEQ is a PAired-eND Assembler for DNA sequences.
  2 KB (239 words) - 18:08, 19 August 2022
• W2rap-contigger
  An Illumina PE genome contig assembler
  2 KB (246 words) - 21:29, 6 December 2019
• Meryl
  ...ear total rewrite of 'meryl' that appeared in both project kmer and Celera Assembler.
  2 KB (254 words) - 22:26, 8 September 2020
• GapCloser
  emerging during the scaffolding process by SOAPdenovo or other assembler,
  2 KB (264 words) - 16:52, 15 August 2022
• Pbipa
  Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was des
  2 KB (268 words) - 21:58, 27 April 2022
• SPAdes
  St. Petersburg genome assembler
  2 KB (280 words) - 15:47, 22 August 2022
• Zorro
  ZORRO is a hybrid sequencing technology assembler. It merges two sets of pre-assembled contigs into a more contiguous and con
  2 KB (284 words) - 17:54, 22 August 2022
• MITObim
  ...lly developed for Illumina data, but thanks to the versatility of the MIRA assembler, MITObim supports in principle also data from the Iontorrent, 454 and PacBi
  3 KB (301 words) - 15:20, 22 April 2020
• Scallop
  Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as
  2 KB (289 words) - 14:44, 26 January 2021
• Haploflow
  Haploflow is a strain-aware viral genome assembler for short read sequence data. It uses a flow algorithm on a deBruijn graph
  2 KB (287 words) - 20:31, 3 January 2022
• SCOP
  be produced by any assembler. The input read data of SCOP is paired-end or
  2 KB (295 words) - 17:31, 15 August 2022
• Raven
  Raven is a de novo genome assembler for long uncorrected reads.
  2 KB (284 words) - 21:14, 20 November 2023
• Compacta
  the assembler to a smaller set of representative sequences, preserving
  3 KB (294 words) - 13:52, 15 August 2022
• Clover
  Clover is a clustering-oriented de novo assembler for Illumina sequences,
  2 KB (296 words) - 13:47, 15 August 2022
• SMARTdenovo
  SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all
  2 KB (296 words) - 21:24, 6 December 2019
• NOVOPlasty
  NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.
  3 KB (310 words) - 21:23, 6 December 2019
• Hifiasm
  Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and
  3 KB (303 words) - 22:23, 27 August 2020
• YASRA
  YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, whi
  3 KB (304 words) - 20:56, 12 August 2022
• Wtdbg
  Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ON
  3 KB (310 words) - 17:44, 22 August 2022
• Oases
  Oases is a de novo transcriptome assembler designed to produce transcripts
  2 KB (293 words) - 17:25, 19 August 2022
• MIRA
  |{{#vardefine:url|http://mira-assembler.sourceforge.net/}} ...ble, CLR not yet. Please visit [http://sourceforge.net/apps/mediawiki/mira-assembler/ the app website] for more details.
  2 KB (313 words) - 20:42, 18 August 2022
• Miniasm
  Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by
  3 KB (306 words) - 20:10, 18 August 2022
• ALLPATHS-LG
  ALLPATHS-LG is a short read assembler. It has been designed to use reads
  2 KB (299 words) - 12:36, 12 August 2022
• Flye
  Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanop
  3 KB (317 words) - 21:20, 6 December 2019
• NextDenovo
  NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strat
  3 KB (312 words) - 18:03, 10 May 2021
• IVA
  IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Ill
  2 KB (300 words) - 16:06, 7 December 2021
• ABySS
  ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful fo
  2 KB (315 words) - 16:17, 19 August 2022
• MarginPolish
  ...is also part of an assembly pipeline which includes an ultrafast nanopore assembler Shasta and a multi-task RNN polisher HELEN. HELEN operates on images genera
  3 KB (320 words) - 21:22, 6 December 2019
• DISCOVAR de novo
  DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimi
  3 KB (326 words) - 14:41, 15 August 2022
• AMOS
  ...resents our primary goal -- to produce A Modular, Open-Source whole genome assembler. Open-source so that everyone is welcome to contribute and help build outst
  3 KB (344 words) - 12:41, 12 August 2022
• MaSuRCA
  Zimin, A. et al. The MaSuRCA genome Assembler. Bioinformatics (2013). doi:10.1093/bioinformatics/btt476
  3 KB (340 words) - 18:24, 18 August 2022
• SHARCGS
  SHort-read Assembler based on Robust Contig-extension for Genomic Sequencing.
  3 KB (313 words) - 22:42, 21 August 2022
• Bridger
  Bridger is an efficient ''de novo'' transcriptome assembler for RNA-Seq data. It expects as input RNA-Seq reads (single or paired) in f
  3 KB (341 words) - 13:14, 15 August 2022
• Hapsembler
  Nilgun Donmez and Michael Brudno (2011) Hapsembler: an assembler for highly polymorphic genomes. In Proceedings of the 15th Annual internati
  3 KB (332 words) - 18:15, 15 August 2022
• IDBA-UD
  IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is
  3 KB (354 words) - 18:40, 15 August 2022
• TriMetAss
  .... It uses Vmatch [2] to extend seed reads (or contigs generated by another assembler) into longer contigs, by iteratively calling Vmatch and Trinity, until some
  3 KB (344 words) - 20:52, 12 August 2022

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