MITObim - mitochondrial baiting and iterative mapping
...ata, but thanks to the versatility of the MIRA assembler, MITObim supports in principle also data from the Iontorrent, 454 and PacBio sequencing platforms. B...2185 days ago
EAGLER: a scaffolding tool for long reads.
...of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads. T...2158 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 PacBio RS long reads. Cerulean v0.1 has been implemented with bact...2157 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...encing technologies, including but not limited to: NGS short reads (Illumina HiSeq) clone-based sequencing (Fosmid or BAC clones) SMRT reads (PacBio) Oxford Nanopore reads 10X...2178 days ago
2170 days ago
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.2169 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-spec...ic filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5)...2169 days ago
WhatsHap: fast and accurate read-based phasing
...hort reads. Features Very accurate results (Martin et al., WhatsHap: fast and accurate read-based phasing) Works well with Illumina, PacBio, Oxford Nanopore and other ty...2165 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...am # use presets (no test data) ./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio genomic reads ./minimap2 -ax..../minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overlap ./minimap2 -x a...2142 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and refer...2126 days ago