Assembly
- 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
- SCRAPE – Shortread Cap3 Random-sample Assembly Program
- TAU 1.4 – Transcriptome Assembly Utility
- Reconciliator 2.0 – The tool for Merging Assemblies
- CodonCode Aligner 4.1.1 – DNA Sequence Assembly & Alignment
- DNA Baser 3.5.4 – DNA Sequence Assembly & Analysis
- ALE – Assembly Likelihood Estimator
- Atlas 2005 – Whole Genome Assembly Suite
- SimAssemblyStage1/2 0.2 – Assembly Alignment of Contigs
- AceParser 1.33 – Parse an Ace file (Phred/Phrap output) into a tab-delimited Assembly Alignment file
- MetaCompass 1.0 – Comparative Assembly of Metagenomic Sequences
- eRGA – enhanced Reference Guided Assembly
- IMAGE 2.33 – Iterative Mapping and Assembly for Gap Elimination
- PASHA 1.0.6 – Parallelized Short Read Assembly
- PAVE 3.6 – Assembling and Viewing ESTs
- GenSeed 1.0.22 – Seed-driven progressive Assembly program
- ShoRAH 0.6 – Short Reads Assembly into Haplotypes
- GS De Novo Assembler – de novo DNA Sequence Assembly
- clview – Assembly File Viewer
- GICL 0.01 – Cluster & Assembly of a large EST/mRNA dataset
- Cleaner 1.03 – Assembly of Informative, Transcript-specific Probe-clusters
- PGAAS 1.0 – Prokaryotic Genome Assembly Assistant System
- WEAV 0.2 – de novo Assembly program for both Genome and RNA
- Phusion 2.1c – Assembly Genome Sequences from Whole Genome Shotgun(WGS) Reads
- Maq 0.7.1 – Mapping and Assembly with Qualities
- Staden 2.0.0b9 – DNA Sequence Assembly , Editing and Analysis
- Anchor 0.3.1 – Post-processing Tools for de novo Assemblies
- OSLay 1.0 – Optimal Syntenic Layout of Unfinished Assemblies
- DNPTrapper 1.0 – Assembly Editing & Visualization Tool
- treecat – Phylogenetic Comparative Assembly
- r2cat – Synteny Plots & Comparative Assembly
- Tracembler – Contig Assembly Tool
- ABBA 2 – Assembly Boosted By Amino acid sequences
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