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Environmental Genomics Group SciLifeLab/KTH Stockholm
By BioStar 753 days agohttps://github.com/envgen - Useful Metagenomics resourcesWebinar on Streamlining large scale analysis using the Strand NGS Pipeline Manager on 24 Feb 2016
By Yeshodari 3244 days agoLive Webinar on Streamlining large scale NGS data analysis using the Strand NGS Pipeline Manager on 24 Feb 2016 Abstract: Strand NGS includes comprehensive workflows for DNA-Seq, RNA-Seq, Small RNA-Seq, ChIP-Seq, MeDIP-Seq, and Methyl-Seq analysis....HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
By Jit 2574 days agonservant.github.io - HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not...MCAT: Motif Combining and Association Tool
By Neel 2171 days agogithub.com - This is a pipeline for finding motifs in fasta files.It can be run from the command line as follows: usage: orange_pipeline_refine.py [-h] [-w W] [--nmotifs NMOTIFS] [--iter ITER] [-c C][-s S] [-d] [-ff] [-v V]positive_seq negative_seq positional...gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
By Rahul Nayak 1795 days agogithub.com - gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and...sunbeam: A robust, extensible metagenomics pipeline
By Jit 1649 days agogithub.com - 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...AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 1380 days agogithub.com - 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...Illumina based assembly pipeline steps !
By Surabhi Chaudhary 1109 days agoGenome assembly pipeline !iMAGine - in silico MetAGenomics pipeline
By BioStar 170 days agogithub.com - iMAGine is a metagenomic workflow which includes filtering, assembling, and binning. This workflow includes the following tools which are needed to be installed in the system. fastp spades assembler QUAST bwa samtools metabat2 CheckMMetaPred2CS
By Manisha Mishra 2852 days agogithub.com - MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component...
