NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was d...2216 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads...2206 days ago
MITObim - mitochondrial baiting and iterative mapping
This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full artic...upports in principle also data from the Iontorrent, 454 and PacB...2203 days ago
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 assembl...nt in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacB...2176 days ago
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 PacB...2175 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 Tools for single molecula sequencing (SMRT) reads. MECAT employs novel a...es 9.5 days to assemble a human genome based on 54x SMRT data, which is 40 times faste...2200 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...se sequencing technologies, including but not limited to: NGS short reads (Illumina HiSeq) clone-based sequencing (Fosmid or BAC clones) SMRT reads (PacBio) Oxford Nanopore reads 10...2196 days ago
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minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.2187 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacB...2187 days ago