GroopM: Metagenomic binning toolset
...s spatio-temoraldynamics (differential coverage) to accurately (and almost automatically)extract population genomes from multi-sample metagenomic datasets. GroopM is largely parameter...2613 days ago
ChromHMM: Chromatin state discovery and characterization
...acterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of vari...computing state enrichments for large-scale functional and annotation datasets ChromHMM facilitates the biol...2570 days ago
CLA: Contig-Layout-Authenticator
...eline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffold...scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool...2554 days ago
npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
...ssemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It also facilitates the real...2536 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
...mic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accur...2535 days ago
Omega2: metagenome assembly pipeline
...ap-layout-consensus assemblers. This indicates Omega can more efficiently assemble longer Illumina reads, and at deeper coverage, for metagenomic datasets.2488 days ago
2503 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...ping step, it takes about 3 minutes to assemble a bacterial genome. Under the default setting, miniasm assembles 9 out of 12 PacBio datasets and 3 out of 4 ONT datasets into a single contig. The 12...2348 days ago
dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
...d, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantif...d genomes since it does not require genome assembly and works on small datasets (< 1X). dnaPipeTE is...2343 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
...ewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data...2325 days ago