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SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2973 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...Picard
By Neel 3750 days agobroadinstitute.github.io - Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF...GAEMR
By Jit 3704 days agowww.broadinstitute.org - The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete...Opera: An optimal genome scaffolding program
By Jit 3173 days agosourceforge.net - Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3164 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...Hawkeye: an interactive visual analytics tool for genome assemblies
By Abhimanyu Singh 2773 days agoamos.sourceforge.net - Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting...Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical...
By BioStar 2205 days agowww.sequenceontology.org - We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers...GenomeTools: The versatile open source genome analysis software
By Neel 1645 days agohttp://genometools.org/ - The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named...CrossMap: program for genome coordinates conversion between different assemblies
By Rahul Nayak 1652 days ago Comments (1)crossmap.sourceforge.net - CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats...Comparative genomics visualisation tools !
By Neel 1630 days agocmdcolin.github.io - Comparative genomics visualisation tools !
