SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:Tags: SLR-superscaffolder, scaffold, assemble, pipeline, stLFR, reads
1534 days ago
gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6733440/Tags: gapFinisher, reliable, gap, filling, pipeline, SSPACE-LongRead, scaffolder, output
1444 days ago
sunbeam: A robust, extensible metagenomics pipeline
Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies, so it doesn't have pre-existing dependencies or admin privileges, and can be deployed on most Linux workstations...Tags: sunbeam, robust, extensible, metagenomics, pipeline
1410 days ago
Tags: WGDdetector, pipeline, etecting, wole, enome, uplication, vents, enome, ranscriptome, nnotations
1375 days ago
PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends on performing a all-vs-all sequence comparison,...Tags: PyParanoid, pipeline, rapid, identification, homologous, gene, families, set, genomes
1354 days ago
SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta featur...Tags: SqueezeMeta, fully, automated, metagenomics, pipeline, reads, bins
1350 days ago
Liftoff: An accurate GFF3/GTF lift over pipeline
Liftoff is a tool that accurately 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 standalone tool that takes two genome assemblies and...Tags: Liftoff, accurate, GFF3, GTF, lift, pipeline
1225 days ago
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
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 improved contig N50 when compared to current state of...Tags: CSA, high-throughput, chromosome-scale, assembly, pipeline, vertebrate, genomes
1145 days ago
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/61467...Tags: AlignGraph2, genome-assisted, reassembly, pipeline, PacBio, long, reads
1141 days ago
Tags: MCscan, pipeline, synteny, plant, annotation, comparative genomics, jcvi
1085 days ago