HipSTR: Haplotype inference and phasing for Short Tandem Repeats
HipSTR was specifically developed to deal with these errors in the hopes...models using an EM algorithm Mining candidate STR alleles from population-scale seque...ized hidden Markov model to align reads to candidate alleles while accounting for ST...1942 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...ts a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also...1916 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio)...ping qualities, multiplexing, and optical/PCR duplicates. All outputs...logenomic and high-throughput sequencing simulator https://jackalope....1802 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...ts a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also...1822 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket rep...tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum)...0 values in the range of dozens of Mb and p...ating chromosome-conformation capture sequencing (Hi-C) data suitable for use...1777 days ago
LRSDAY: Long-read Sequencing Data Analysis for Yeasts
Long-read sequencing technologies have become increasingly popular in genome projects du...olving complex genomic regions. As a leading model organism with small genome size and great biotechnol...1770 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 t...sing capacity of existing algorithms and compute infrastructures. In t...e use of hardware/software co-design and h...introduce Shouji, a highly parallel and accurate pre-alignment filter that r...1701 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...overed at or above a given threshold for each chromosome and g...given thresholds.A summary of mean depths per chromosome and within...1688 days ago
NextDenovo: string graph-based de novo assembler for TGS long reads
NextDenovo is a string graph-based de novo assembler...ntly less computing resources and storages. After assembly, the...two core modules: NextCorrect and NextGraph. NextCorrect can be...reads with approximately 15% seque...imap2 for adapting input and output and producing more sensitive...1639 days ago
ngs-bits - Short-read sequencing tools
Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for Windows1627 days ago