BioStar
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Understanding pango networks !
By Abhi 1133 days agowww.pango.network - In the vast majority of instances it is expected that Pango lineage names and designations will conform to the following rules. These rules also act as guidelines for the decisions made by the Lineage Designation...Bioinformatics Training Material !
By BioStar 616 days agoglittr.org - Glittr is a curated list of bioinformatics training material.All material is: In a GitHub or GitLab repository Free to use Written in markdown or similar NOTE: This list of courses is selected only based on the above criteria.There...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 2553 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 2452 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 2384 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 2375 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...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2357 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...FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
By Jit 2287 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 2285 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...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2227 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...
