EAGLER: a scaffolding tool for long reads.
EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are use...2161 days ago
Cerulean: A hybrid assembly using high throughput short and long reads
...ed using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has b...013). Cerulean: A hybrid assembly using high throughput short and long reads. arXiv preprint arXiv:1...2160 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 fro...vely low identity requirement so that a long read region can be aligned to...comparable accuracy. The HALC corrected long reads can thus result in 11.4...2157 days ago
2154 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
...both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs....2153 days ago
Digest: In silico restriction digest of complete genomes
...tic genomes. When the number of fragments is bellow 50, Pulse Field gel Electrophoresis (PFGE) is simulated. A tool for restriction digest of longuser's sequences is available....2182 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...16 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilo...aghi M, Amini S, L Gunderson K, Steemers FJ, Shendure J#. In vitro, long-range sequence information fo...2182 days ago
LAMSA: fast split read alignment with long approximate matches
LAMSA (Long Approximate Matches-based Split Align...SV events. It is well-suited to align long reads (over thousands of base...ially splits the read into relatively long fragments and co-linearly ali...ally faster than the state-of-the-art long read aligners; mean-while, it...2181 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...n (Hi-C) reads high-coverage sequencing (>40x coverage-per-SNP) using above technologies combinations of the above technologies (e.g. scaffold long reads with Hi-C reads) See b...2181 days ago
TULIP - The Uncorrected Long read Integration Pipeline
...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 short seeds,...2181 days ago