:: DESCRIPTION
FastqCLS is a robust FASTQ-specific compressor for recent generation data via score-based reordering.
:: DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lee D, Song G.
FastqCLS: a FASTQ Compressor for Long-read Sequencing via read reordering using a novel scoring model.
Bioinformatics. 2021 Oct 8:btab696. doi: 10.1093/bioinformatics/btab696. Epub ahead of print. PMID: 34623374.
:: DESCRIPTION
NextSV is an automated pipeline for structrual variation detection from long-read sequencing. NextSV uses two aligners (Minimap2 and NGMLR) to do read mapping and uses Sniffles to do SV calling.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fang L, Hu J, Wang D, Wang K.
NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data.
BMCBioinformatics. 2018 May 23;19(1):180. doi: 10.1186/s12859-018-2207-1. PMID: 29792160; PMCID: PMC5966861.
:: DESCRIPTION
NanoMod is a novel computational tool for the detection of DNA modifications using Nanopore long-read sequencing data. The evaluation on simulation data with different types of modifications and on a methylation data of E. coli suggested that NanoMod achieved better performance than other existing tools in detecting modifications without training data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Qian Liu, Daniela C. Georgieva, Dieter Egli and Kai Wang.
NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data.
BMC Genomics 20(1):78, 2019. doi: 10.1186/s12864-018-5372-8.
:: DESCRIPTION
PBSuite includes:
PBJelly – the genome upgrading tool.
PBHoney – the structural variation discovery tool
PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles.
PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp).
::DEVELOPER
Human Genome Sequencing Center, Baylor College of Medicine
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2014 Jun 10;15:180. doi: 10.1186/1471-2105-15-180.
PBHoney: identifying genomic variants via long-read discordance and interrupted mapping.
English AC1, Salerno WJ, Reid JG.
English AC, Richards S, Han Y, Wang M, Vee V, et al. (2012)
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology.
PLoS ONE 7(11): e47768. doi:10.1371/journal.pone.0047768
