Jit
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Understanding your reads and mapping !
By Neel 1761 days agobioinformatics-core-shared-training.github.io - One of the best tutorial for beginners ... https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.htmlminiasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 2554 days agogithub.com - 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. Different from mainstream...
Run miniasm assembler on nanopore reads !
Last updated 2534 days ago by Jit Comments (5)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. Different from mainstream...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 2396 days agogithub.com - 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 and does not require them to be error-corrected. After...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2385 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2359 days agojapsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
By Rahul Nayak 1655 days agogithub.com - LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds...SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2286 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2259 days agogithub.com - Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Neel 2190 days agogithub.com - Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful...
