LAMSA: fast split read alignment with long approximate matches
...gy. That is, LAMSA initially splits the read into relatively long fragments and co-linearly align them to solve the small variations or sequencing errors, and mitigate the effect of r...2197 days ago
2148 days ago
GFinisher: a new strategy to refine and finish bacterial genome assemblies
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/sca...2125 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...oterights error profile. The algorithm learns a posterior transition/emission probability distribution for each long read and uses this to correct errors in these reads. Using dataset...2099 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...ads require a high depth of coverage. This motivates the development of hybrid approaches that leverage the high quality of short reads to correct errors in long reads.We introduce Co...2099 days ago
LoRMA: A tool for correcting sequencing errors in long reads
An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn...2082 days ago
COSINE: non-seeding method for mapping long noisy sequences
Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors.2033 days ago
Hawkeye: an interactive visual analytics tool for genome assemblies
...emains an inexact science, and genome sequences can contain significant errors if they are not carefully exa...nome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels...1965 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
...bsp;is therefore not only fast, but also as accurate as existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchma...1960 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an...1943 days ago