:: DESCRIPTION
SALSA is a tool to scaffold long read assemblies with Hi-C.
::DEVELOPER
MarBL (Maryland Bioinformatics Labs)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ghurye J, Pop M, Koren S, Bickhart D, Chin CS.
Scaffolding of long read assemblies using long range contact information.
BMC Genomics. 2017 Jul 12;18(1):527. doi: 10.1186/s12864-017-3879-z. PMID: 28701198; PMCID: PMC5508778.
:: DESCRIPTION
ARCS is a genomics software for scaffolding genome assembly drafts using linked or long reads.
::DEVELOPER
Canada’s Michael Smith Genome Sciences Centre
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Coombe L, Zhang J, Vandervalk BP, Chu J, Jackman SD, Birol I, Warren RL.
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.
BMC Bioinformatics. 2018 Jun 20;19(1):234. doi: 10.1186/s12859-018-2243-x. PMID: 29925315; PMCID: PMC6011487.
:: DESCRIPTION
BELLA is a computationally efficient and highly accurate long-read to long-read aligner and overlapper.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper
Giulia Guidi, Marquita Ellis, Daniel Rokhsar, Katherine Yelick, Aydın Buluç
bioRxiv 464420; doi: https://doi.org/10.1101/464420
:: DESCRIPTION
LRSDAY is a highly transparent, automated and powerful computational framework for high-quality genome assembly and annotation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yue JX, Liti G.
Long-read sequencing data analysis for yeasts.
Nat Protoc. 2018 Jun;13(6):1213-1231. doi: 10.1038/nprot.2018.025. Epub 2018 May 3. PMID: 29725120.
:: DESCRIPTION
rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio’s Single Molecule Read-time (SMRT) sequencing reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
rHAT: fast alignment of noisy long reads with regional hashing.
Liu B, Guan D, Teng M, Wang Y.
Bioinformatics. 2015 Nov 14. pii: btv662.
:: DESCRIPTION
BWA (Burrows-Wheeler Aligner) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Li H. and Durbin R. (2009)
Fast and accurate short read alignment with Burrows-Wheeler Transform.
Bioinformatics, 25:1754-60.
:: DESCRIPTION
NanoMark is a system for benchmarking DNA assembly tools, based on 3rd generation sequencers.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads.
Sović I, Križanović K, Skala K, Šikić M.
Bioinformatics. 2016 May 9. pii: btw237.
:: DESCRIPTION
FinisherSC is a repeat-aware and scalable tool for upgrading de-novo assembly using long reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
FinisherSC : A repeat-aware tool for upgrading de-novo assembly using long reads.
Lam KK, LaButti K, Khalak A, Tse D.
Bioinformatics. 2015 Jun 3. pii: btv280.
:: DESCRIPTION
LongGF is a fast computational tool to efficiently detect candidate gene fusion from long-read RNA-seq data, including cDNA sequencing data and direct mRNA sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Liu Q, Hu Y, Stucky A, Fang L, Zhong JF, Wang K.
LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.
BMC Genomics. 2020 Dec 29;21(Suppl 11):793. doi: 10.1186/s12864-020-07207-4. PMID: 33372596; PMCID: PMC7771079.
