Jit
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Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Jit 1750 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 2532 days agoLongest read of 1mb achievements with NanoporeNanoPack: visualizing and processing long-read sequencing data
By Jit 2298 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 2377 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 1982 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 2288 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....Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 1969 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
By Jit 1431 days agogithub.com - Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce...dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
By Rahul Nayak 2549 days agogithub.com - dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...3d-dna: 3D de novo assembly (3D DNA) pipeline
By Jit 2523 days agogithub.com - This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise...
