Jit
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LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 2414 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...
Tools to access the quality of your assembled genome !
Last updated 136 days ago by LEGEFASTA VALIDATOR + SEQKIT RMDUP: FASTA validation GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation ASSEMBLATHON STATS: Assembly statistics GENOMETOOLS GT STAT: Annotation statistics NCBI FCS ADAPTOR: Adaptor contamination pass/fail NCBI...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 2574 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...ALF--a simulation framework for genome evolution.
By Jit 1888 days agohttp://alfsim.org/#index - Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be found in the following article: Daniel A Dalquen,...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 1787 days agogithub.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...Flanker
By Rahul Nayak 1394 days agogithub.com - Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be...VCF Compare !
By Rahul Nayak 1068 days agowiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...gbtools: Interactive Visualization of Metagenome Bins in R
By Jit 2828 days agojournal.frontiersin.org - We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of...fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 2414 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...GPOPSIM: a simulation tool for whole-genome genetic data
By Jit 2531 days agogithub.com - GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can...
