samstat.sourceforge.net - SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads...
sourceforge.net - EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies...
github.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...
github.com - 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 Windows
github.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...
github.com - Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a...
github.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...
github.com - Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules:...
ncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...
github.com - The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed...