RNA-seq Analysis Workshop Course Materials
...an be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species...r the species of interest is available. In this case one would need to assemble the reads into transcripts us...2127 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...by only considering those reads which should assemble together. Reducing/removing...ive, but rather when the researcher wishes to assemble discreet 'targets' contained...ch the researcher wishes to de novo assemble specific content and a set of...2104 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...ved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly frag...2079 days ago
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Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
...egment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Ra...2019 days ago
Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by Pa...Bio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error corr...termediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb&n...2019 days ago
BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly...2013 days ago
SIMBA: a Genome Assembly Project Management System
...or Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced w...1978 days ago
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StringTie Transcript assembly and quantification for RNA-Seq
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into p...n optional de novo assembly step to assemble and quantitate full-length tr...ads that can also be used by other transcript assemblers, but also alignments of lon...1420 days ago