Jit
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Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Jit 1792 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 in image classification. Unlike...1mb long DNA with Nanopore technology
By Jit 2574 days agoLongest read of 1mb achievements with NanoporeNanoPack: visualizing and processing long-read sequencing data
By Jit 2340 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2419 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...FLAS: fast and high throughput algorithm for PacBio long read self-correction.
By Jit 2025 days agogithub.com - FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2330 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
By Jit 2573 days agowww.ncbi.nlm.nih.gov - While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes from the...RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
By LEGE 1642 days agogithub.com - RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-end bulk RNA-seq (strand-specific/agnostic) paired-end single-cell RNA-seq...Unicycler: Hybrid assembly pipeline for bacterial genomes
By Jit 2614 days agogithub.com - Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs...
