LRCstats – Evaluating Long Reads Correction tools

LRCstats

:: DESCRIPTION

LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

LRCstats

:: MORE INFORMATION

Citation

La S, Haghshenas E, Chauve C.
LRCstats, a tool for evaluating long reads correction methods.
Bioinformatics. 2017 Nov 15;33(22):3652-3654. doi: 10.1093/bioinformatics/btx489. PMID: 29036421.

HASLR – Fast Hybrid Assembly of Long Reads

HASLR

:: DESCRIPTION

HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

HASLR

:: MORE INFORMATION

Citation

Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F.
HASLR: Fast Hybrid Assembly of Long Reads.
iScience. 2020 Aug 21;23(8):101389. doi: 10.1016/j.isci.2020.101389. Epub 2020 Jul 25. PMID: 32781410; PMCID: PMC7419660.

Freddie v0.3.1 – Long Reads Isoform Discovery Tool

Freddie v0.3.1

:: DESCRIPTION

Freddie: Annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
conda
Python

:: DOWNLOAD

Freddie

:: MORE INFORMATION

Citation

Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms

Baraa Orabi, Brian McConeghy, Cedric Chauve, Faraz Hach

bioRxiv 2021.01.20.427493; doi: https://doi.org/10.1101/2021.01.20.427493

Tigmint v1.2.4 – Correct Misassemblies using linked AND long reads

Tigmint v1.2.4

:: DESCRIPTION

Tigmint identifies and corrects misassemblies in genomes using linked (e.g. MGI’s stLFR, 10x Genomics Chromium) or long (e.g. Oxford Nanopore Technologies long reads) DNA sequencing reads.

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Tigmint

:: MORE INFORMATION

Citation

Jackman SD, Coombe L, Chu J, Warren RL, Vandervalk BP, Yeo S, Xue Z, Mohamadi H, Bohlmann J, Jones SJM, Birol I.
Tigmint: correcting assembly errors using linked reads from large molecules.
BMC Bioinformatics. 2018 Oct 26;19(1):393. doi: 10.1186/s12859-018-2425-6. PMID: 30367597; PMCID: PMC6204047.

Straglr v1.1.1 – Short-tandem Repeat Genotyping using long Reads

Straglr v1.1.1

:: DESCRIPTION

Straglr is a new software tool for targeted genotyping and repeat expansion detection

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Python

:: DOWNLOAD

Straglr

:: MORE INFORMATION

Citation

Chiu R, Rajan-Babu IS, Friedman JM, Birol I.
Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences.
Genome Biol. 2021 Aug 13;22(1):224. doi: 10.1186/s13059-021-02447-3. PMID: 34389037; PMCID: PMC8361843.

LongStitch v1.0.1 – Correct and Scaffold Assemblies using long Reads

LongStitch v1.0.1

:: DESCRIPTION

LongStitch is a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads.

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

LongStitch

:: MORE INFORMATION

Citation

Coombe L, Li JX, Lo T, Wong J, Nikolic V, Warren RL, Birol I.
LongStitch: high-quality genome assembly correction and scaffolding using long reads.
BMC Bioinformatics. 2021 Oct 30;22(1):534. doi: 10.1186/s12859-021-04451-7. PMID: 34717540.

MAIRA 0.1.7 – Real-time Taxonomic and Functional analysis of long Reads on a laptop

MAIRA 0.1.7

:: DESCRIPTION

MAIRA is a new standalone program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop without internet access. The program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph.

::DEVELOPER

the Algorithms in Bioinformatics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows

:: DOWNLOAD

MAIRA

:: MORE INFORMATION

Citation

Albrecht B, Bağcı C, Huson DH.
MAIRA- real-time taxonomic and functional analysis of long reads on a laptop.
BMC Bioinformatics. 2020 Sep 17;21(Suppl 13):390. doi: 10.1186/s12859-020-03684-2. PMID: 32938391; PMCID: PMC7495841.

miniasm v0.3- Fast Overlapped-based de novo Assembler for Noisy long Reads

miniasm v0.3

:: DESCRIPTION

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Miniasm

:: MORE INFORMATION

Citation

Li H.
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
Bioinformatics. 2016 Jul 15;32(14):2103-10. doi: 10.1093/bioinformatics/btw152. Epub 2016 Mar 19. PMID: 27153593; PMCID: PMC4937194.