Cerulean: A hybrid assembly using high throughput short and long reads
Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented wi...n: A hybrid assembly using high throughput short and long reads. arX...2218 days ago
HALC: High throughput algorithm for long read error correction
HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same...identity requirement so that a long read region can be aligned to at l...le accuracy. The HALC corrected long reads can thus result in 11.4-60.7% long...2215 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome ass...implements for genome assembly: PRICE uses paired-read information to iteratively in...ntigs. Initially, those contigs can be individual reads from...2213 days ago
2212 days ago
2209 days ago
Many-to-many pairwise alignments of two sequence sets
needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal gl...y exploring all possible alignments and choosing the best. A scoring matrix is read that...2204 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly To...le molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more...nomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT t...2243 days ago
2239 days ago
LAMSA: fast split read alignment with long approximate matches
LAMSA (Long Approximate Matches-based Split Aligner) is a novel split al...ents. It is well-suited to align long reads (over thousands of base-pair.... That is, LAMSA initially splits the read into relatively long fragment...ated and real datasets having various read lengt...2239 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with...s are specialized for specific read technologies or protocols, wi...t not limited to: NGS short reads (Illumina HiSeq) clone-base...id or BAC clones) SMRT reads (PacBio) O...2239 days ago