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LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 2853 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...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3012 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...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2843 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2529 days agogithub.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...Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 2074 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences
By LEGE 187 days agogithub.com - Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.BUSCO
By Jitendra Narayan 3679 days agohttp://busco.ezlab.org/ - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/BRAKER: pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and...
By Jit 3473 days agobioinf.uni-greifswald.de - Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction...Download assemblies from NCBI
By Bulbul 3217 days ago Comments (1)A new “Download assemblies” button is now available in the Assembly database. This makes it easy to download data for multiple genomes without having to write scripts.GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
By Jit 2853 days agogithub.com - This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this...
