Assembly Tools
- rectangles 2.0 – Rectangle Graph for Repeat Resolution in Genome Assembly
- SPAdes 2.4 – Single-cell Genome Assembler
- QUAST 2.1 – Quality Assessment Tool for Genome Assemblies
- EBARDenovo 1.2.2 – Highly-accurate de novo Assembler of Paired-end RNA-Seq
- Minia 1.4961 – Short-read Assembler based on a de Bruijn graph
- scarpa 0.22 – Scaffolding Reads with Practical Algorithms
- hapsembler 2.11 – Haplotype-specific Genome Assembly Toolkit
- Trinity 20130225 – RNA-Seq De novo Assembly
- CLC Genomics Workbench 6.0.3 – Assembly & Analysis of Sequencing Data
- Tablet 1.13.05.02 – Next Generation Sequence Assembly Visualization
- Ray 2.2.0 – Parallel Genome Assemblies for Parallel DNA sequencing
- Arachne 4.6233 – Whole-genome Shotgun Assembler
- Velvet 1.2.09 – Sequence Assembler for Very Short Reads
- SCRAPE – Shortread Cap3 Random-sample Assembly Program
- TAU 1.4 – Transcriptome Assembly Utility
- Phred/Phrap/Consed 24.0 – DNA Sequence Assembler & Finishing Tools
- PRICE 1.0.1 – de novo Genome Assembler
- mapsembler 2_20130509 – Targetted Assembly of Short Sequence Reads
- Reconciliator 2.0 – The tool for Merging Assemblies
- PhrapUMD 2 – Modified version of Phrap
- ABySS 1.3.5 – de novo, parallel, paired-end Sequence Assembler
- MaSuRCA 1.9.5 – Whole Genome Short Read Assembler
- SR-ASM – DNA Assembly of the Short Sequences coming from 454 sequencer
- Cufflinks 2.1.1 – Transcript Assembler & Abundance Estimator for RNA-Seq
- Scaffold_builder v2 – Order Contigs generated by draft sequencing along a Reference Sequence
- EagleView 2.2 – Genome Assembler Viewer
- DNA Dragon 1.5.6 build1 – DNA Sequence Contig Assembler Software
- CodonCode Aligner 4.1.1 – DNA Sequence Assembly & Alignment
- DNA Baser 3.5.4 – DNA Sequence Assembly & Analysis
- ALE – Assembly Likelihood Estimator
- ATLAS GapFill 2.2 – Deals with the Repetitive Gap Assembly problem
- Edena v3 dev130110 – De Novo Short Reads Assembler
- GeneStitch 1.1 – Network Matching Algorithm to Gene Assembly
- Atlas 2005 – Whole Genome Assembly Suite
- Gossamer 1.3.0 – A Space-Efficient Genome Assembler
- SimAssemblyStage1/2 0.2 – Assembly Alignment of Contigs
- MetaCompass 1.0 – Comparative Assembly of Metagenomic Sequences
- V-FAT 1.1 – Automated Finishing, Annotation, and QA tool for Viral Assemblies
- VICUNA 1.1 – de novo Assembler for Ultra-deep Sequence data
- RC454 1.2 – Read Alignment and Error Correction tool for Cleaning 454 Reads of Process Errors
- AV454 1.0 – de novo Consensus Assembler designed for reads derived from diverse Viral Populations
- GapFiller – Close Gaps within Pre-assembled Scaffolds
- SSPACE 1.2 – Scaffolding pre-assembled Contigs using Paired-read data
- SCUBAT – Scaffolding Contigs using BLAT and Transcripts
- eRGA – enhanced Reference Guided Assembly
- GapFiller – Closing the Gap within Paired Reads
- GAM-NGS – Genome Assemblies Merger for Next Generation Sequencing
- QSRA 1.0 – Quality-value guided de novo Short Read Assembler
- Sequencher 5.1 – DNA Sequence Assembly and Analysis
- IMAGE 2.33 – Iterative Mapping and Assembly for Gap Elimination
- PASHA 1.0.6 – Parallelized Short Read Assembly
- PAGIT 1.01 – Post Assembly Genome Improvement Toolkit
- PAVE 3.6 – Assembling and Viewing ESTs
- GenSeed 1.0.22 – Seed-driven progressive Assembly program
- MIRA 3.4.1.1 – Whole Genome Shotgun and EST Sequence Assembler
- TASR 1.4 – Targeted Assembly of Sequence Reads
- GAM – Genome Assemblies Merger
- Velvet-SC 0.7.62 – Velvet modified for Single Cell reads
- GRASS 0.003 – GeneRic ASembly Scaffolder
- MAIA 0.5 – Integrating Genome Assemblies
- SEQuel 1.0.2 – Improving the Accuracy of Genome Assemblies
- MAP 20121108 – A de novo Metagenomic Assembly program for Shotgun DNA reads
- SeqCons 1.0 – de novo and reference-guided Sequence Assembly
- Trans-ABySS 1.4.4 – Analyze ABySS multi-k-assembled Shotgun Transcriptome Data.
- ShoRAH 0.6 – Short Reads Assembly into Haplotypes
- BioLign 4.0.6 – Assembly Editor
- Pasqual 1.0 – Parallel de Novo Genome Sequence Assembler
- Quake 0.3.4 – Detect & Correct Substitution Sequencing Errors in WGS Data Sets
- ABySS-Explorer 1.3.4 – Sequence Assembly Visualization Tool
- Taipan 20090515 – Fast Hybrid Short-read Assembly tool
- Meta-IDBA 0.19 – De Bruijn Graph De Novo short read assembler designed for de novo Metagenomic Assembly
- T-IDBA 0.20 – De Bruijn Graph De Novo Short Read Assembler for Transcriptome
- IDBA-UD 1.09 – De Bruijn Graph De Novo Assembler with Highly Uneven Sequencing Depth
- IDBA 0.20 – De Bruijn Graph De Novo Assembler for sequence assembly
- GS De Novo Assembler – de novo DNA Sequence Assembly
- Oases 0.2.08 – De novo Transcriptome Assembler for very short reads
- RePS 2.0 – WGS Sequence Assembler
- FLASH 1.0.3 – Fast Length Adjustment of SHort reads
- clview – Assembly File Viewer
- ViSpA 01 – Viral Spectrum Assembler
- PGAAS 1.0 – Prokaryotic Genome Assembly Assistant System
- WEAV 0.2 – de novo Assembly program for both Genome and RNA
- SHORTY 2.0 – de novo Assembler
- MASS 1.2 – Map and Assemble Sequence Date
- VCAKE 2.0 – Genetic Sequence Assembler
- RMAP 2.05 – Short-read Mapping
- SHARCGS – SHort read Assembler based on Robust Contig extension for Genome Sequencing
- Phusion 2.1c – Assembly Genome Sequences from Whole Genome Shotgun(WGS) Reads
- ABACAS 1.3.1 – Algorithm Based Automatic Contiguation of Assembled Sequences
- LaneCheck 0.0.1 – Checking Lane Identity
- Celera Assembler 7.0 – Whole Genome Shotgun Assembler
- CAP3 / PCAP – Sequence and Genome Assembly Programs
- FPC 9.4 – Build Contigs from Fingerprinted Clones
- CSPS 2.0.0 – Comparative Shotgun Protein Sequencing
- AMOS 3.1.0 – Whole Genome Shotgun Assembler
- THOR 1.0 – Assemble Target Genomic Sequence Orthologs
- SSAKE 3.8 – Assembling Millions of short DNA Sequences
- SAM 1.0 – Sequence Assembly Manager
- FASSI 1.0 – Fingerprint and ASSembly Incorporation
- Anchor 0.3.1 – Post-processing Tools for de novo Assemblies
- FuLinkA 0.5 – Fuzzy Linking Assembler for Genomic Sequences
- Transcriptome Assembler – Transcriptome Assembly used in RNA-seq of 16 Mammalian Species
- KARMA 0.9 – Aligner for Mapping Shotgun Sequencer FASTQ Read
- SeqAssem 200807- Molecular Sequence Assembly
- OSLay 1.0 – Optimal Syntenic Layout of Unfinished Assemblies
- LOCAS / SUPERLOCAS – Low-coverage Short-read Assembler
- DNPTrapper 1.0 – Assembly Editing & Visualization Tool
- AmosCmp16Spipeline 20090918 – Assemble 16S rRNA Sequencing Reads
- ALLPATHS-LG – Whole Genome Shotgun Assembler
- treecat – Phylogenetic Comparative Assembly
- r2cat – Synteny Plots & Comparative Assembly
- Tracembler – Contig Assembly Tool
- SOMA 2.0 – Scaffolding using Optical Restriction Mapping
- AutoEditor 1.20 – Automated Correction of Genome Sequence Errors
- ABBA 2 – Assembly Boosted By Amino acid sequences
- Lucy 2.19p-R8 – DNA Sequence Quality & Vector Trimming
Recent Comments