Poonam Mahapatra
Bioinformatics Researcher
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miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 2555 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...Reference-free prediction of rearrangement breakpoint reads
By Neel 2454 days agocode.google.com - lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing...TAREAN: A computational tool for identification and characterization of satellite DNA from...
By Surabhi Chaudhary 2386 days agobitbucket.org - TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their...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...FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
By Jit 2289 days agogithub.com - Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python...LRCstats: a tool for evaluating long reads correction methods
By Aaryan Lokwani 2287 days agogithub.com - 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. The reads produced by third generation...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2229 days agosourceforge.net - Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like...wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
By BioStar 2121 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly...NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 1786 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...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...
