Reference-free prediction of rearrangement breakpoint reads
lideSort-BPR ( b reak p oint r eads) is based on a fast algor...retical analyses of the number of neighboring reads. When applied to a dataset with a sequencing...2302 days ago
SciLifeLab tutorial for bioinformatics analysis !
SciLifeLab is a national center for molecular biosciences with focus on health and environm...ions for Life Scientists 2016 November - Uppsala2017 Mars - Uppsala Single cell RNA sequencing...2262 days ago
2260 days ago
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 sensiti...nes to compute precise alignments. The gap model allows ngmlr to account for both the sequencing...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...2244 days ago
MITObim - mitochondrial baiting and iterative mapping
This document contains instructions on how to use the MITObim pipeline described in Hahn et...s in principle also data from the Iontorrent, 454 and PacBio sequencing...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 populat...ith several alignment strategies, enable rapid and accurate alignment of sequencing...2241 days ago
MIX: Combining multiple assemblies from NGS data
Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome f...2241 days ago
Porechop: tool for finding and removing adapters from Oxford Nanopore reads
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its midd...2220 days ago