Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new o...elationships among the draft and reference genomes and libraries of paired-end reads....2304 days ago
Reference-free prediction of rearrangement breakpoint reads
lideSort-BPR ( b reak p oint r eads) is based...rithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset wi...s, and yet produces fewer false-positive reads....2302 days ago
2260 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
...ickly and correctly align the reads, including those spanning (co...er search to find approximate mapping locations for a read and th...for longer gaps less than for shorter ones to compute precise ali...rch helps to detect and split reads that cannot be aligned linearly...2254 days ago
ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-82249 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 a...2245 days ago
2245 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 article can be found here. Kindly cite the article i...2241 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling...gh a novel algorithm that can be proved preserving all phasing paths from reads and paired-end reads,...2241 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as...gies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is ca...2241 days ago