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Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit,...
By Neel 2310 days agowww.phrap.org - Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence...BEAR: Better Emulation for Artificial Reads
By BioStar 699 days agogithub.com - Created by Stephen Johnson, Brett Trost, Dr. Jeffrey R. Long, Dr. Anthony Kusalik University of Saskatchewan, Department of Computer Science BEAR is intended to be an easy-to-use collection of scripts for generating simulated WGS metagenomic reads...SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2912 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...Next Generation Sequencing (NGS) Tutorials
By Jitendra Narayan 4668 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 3771 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 3578 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 3116 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 2727 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 1283 days agohttps://github.com/envgen - Useful Metagenomics resourcesVariant Calling Pipeline
By LEGE 594 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...
