rHAT: a seed-and-extension-based noisy long read alignment tool
rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.2061 days ago
2056 days ago
Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
...7.pdf. The prepint version is found on http://www.biorxiv.org/content/early/2017/08/09/173872 It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/p...2011 days ago
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
...igh error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the r...1996 days ago
BLAST options, setting and defaults
BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et...ch is the best choice. Another sequence alignment tool that may yield different...lt = 25 default = 25 default = 25 Max alignments:number of alignments to show...1983 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
...implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints. SiLiX...1981 days ago
Versatile genome assembly evaluation with QUAST-LG
...features (see CHANGES for all): Significant speedup achieved by both use of new fast aligner (minimap2) and the refactoring of alignment analyzing modules New k...1972 days ago
ZENBU: a collaborative, omics data integration and interactive visualization system
...loration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded...1958 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
...It is based on the novel idea of pseudoalignment for rapidly determining...of reads with targets, without the need for alignment. On benchmarks with standard...f takes less than 10 minutes to build. Pseudoalignment of reads preserves the key in...1955 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
...algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of LTR pair candidates to get alignment boundaries. These boundaries...1949 days ago