jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
jackalope simply and efficiently simulates (i) variants from...om Pacific Biosciences These simulations include sequencing errors, mapping qualities, mu...wift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope....1804 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
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 bacte...1824 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket repository. TRI...loid genomes. A protocol for generating chromosome-conformation capture sequencing (Hi-C) data suitable for use...1779 days ago
Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences
Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searchi...1772 days ago
LRSDAY: Long-read Sequencing Data Analysis for Yeasts
Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism...1772 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use...1703 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be...1690 days ago
simuG: a general-purpose genome simulator
Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightwe...1679 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high e...1674 days ago
NextDenovo: string graph-based de novo assembler for TGS long reads
NextDenovo is a string graph-based de novo assembler for TGS long reads. It us...ph. NextCorrect can be used to correct TGS long reads with approximately 15% sequencing errors, and NextGraph can be...1641 days ago