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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via...
By Jit 2768 days agogithub.com - MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to...CANU genome assembly parameters !
By Rahul Nayak 2714 days agoChoose the appropriate parameters to run Canu and run it.NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
By BioStar 2697 days agogithub.com - NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file...SDA: Long-read sequence and assembly of segmental duplications
By Jit 2657 days agowww.nature.com - Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of...StringTie Transcript assembly and quantification for RNA-Seq
By Jit 2195 days agoccb.jhu.edu - StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length...MEC: Contig Misassembly Correction
By BioStar 2321 days agogithub.com - MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on...SvABA: Structural variation and indel detection by local assembly
By Jit 2286 days agogithub.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 2234 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...Software for genome assembly !
By LEGE 2113 days agoList of bioinformatics tools/Software Website References for genome assembly:CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
By Jit 1921 days agogithub.com - The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the contigs and thus support the assembly process. This typically results in...
