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Next Generation Sequencing (NGS) Tutorials
By Jitendra Narayan 4107 days ago Comments (31)chagall.med.cornell.edu - Institute of computational biomedicine, Cornell University provide an NGS workshop tutorial at http://chagall.med.cornell.edu/NGScourse/ You can also add your favourite NGS educational material, or workshop tutorial by commenting on this...BUSCO
By Jitendra Narayan 3210 days agohttp://busco.ezlab.org/ - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/TEannot
By Jit 3017 days agourgi.versailles.inra.fr - We advise to run first the TEdenovo pipeline but it is not compulsory. We suppose you begin by running the TEannot pipeline on the example provided in the directory "db/" rather than directly on your own genomic sequences. Thus, from now on, the...TULIP - The Uncorrected Long read Itegration Pipeline
By Jit 2555 days agogithub.com - #Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel) TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional...Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
By Rahul Nayak 2166 days agobitbucket.org - Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an...Environmental Genomics Group SciLifeLab/KTH Stockholm
By BioStar 722 days agohttps://github.com/envgen - Useful Metagenomics resourcesVariant Calling Pipeline
By LEGE 33 days agogithub.com - The variantcalling.nf nextflow script will take any number of samples with paired-end reads in FASTQ format, map reads using Bowtie2, process BAM files, and finally call variants using BCFtools v1.21 and/or Freebayes v1.3.6. If part of the...DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
By Jit 2564 days agohttps://dfast.nig.ac.jp/ - We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its...3d-dna: 3D de novo assembly (3D DNA) pipeline
By Jit 2520 days agogithub.com - This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise...MCAT: Motif Combining and Association Tool
By Neel 2139 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...
