TULIP - The Uncorrected Long read Itegration Pipeline
...These are very much intended as prototypes, and additional components and/or implementations are likely to follow. Tulipseed takes as input alignments files of long reads to sparse...2398 days ago
Ribbon: Visualizing complex genome alignments and structural variation:
Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each t...2392 days ago
ACANA: An accurate and consistent alignment tool for DNA sequences
...e moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts to combine the best of local and global alignments algorithms in searching for e...2385 days ago
kraken: A universal genomic coordinate translator for comparative genomics
If you planning on conducting a study involving dozens of large genomes, then you do not have to run all pairwise synteny alignments .. simply try kraken: A universal genomic coordinate translator for comparative genomics2384 days ago
Harvest: a suite of core-genome alignment and visualization tools
...ation detection, and phylogenetic trees. Tools Parsnp - Core-genome alignment and analysis Gingr - Interactive visualization of alignments, trees and variants HarvestT...2383 days ago
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PASA: Gene Structure Annotation and Analysis
...ASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript seque...icing variations supported by the transcript alignments.2364 days ago
zPicture: A dynamic blastz alignment visualization
zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.2329 days ago
xmatchview: smith-waterman alignment visualization
...mats. xmatchview and xmatchview-conifer are written in python and run on linux and windows. They serve as visual tools for analyzing cross_match alignments. Cross_match (Green, P. (1994...2363 days ago
LRCstats: Long Read Correction Statistics
...s produced by simulators (such as SimLoRD or PBSim) where the two-way alignments between the uncorrected long...d then aligning the corrected long reads (cLR) to the Ref-uLR two-way alignments to create three-way alignment...2355 days ago