2171 days ago
String graph based genome assembly software and tools !
...which are often collapsed by other assemblers. Its ultimate goal is to find a minimal set of unitigs to represent all the information in raw reads. If you want to learn...2379 days ago
CANU genome assembly parameters !
...te the error correction process. canu -p test_asmbl \ -d asm_test3 \ genomeSize=2m \ -maxThreads=2 useGrid=false \ -pacbio-raw \ ~/pacbio/dna/sample_reads.f...1996 days ago
3704 days ago
InfoGenomeR: Integrative reconstruction of cancer genome karyotypes
InfoGenomeR is the Integrative Framework for Genome Reconstruction that uses a breakpoint graph to model the connectivity among genomic segments at the genome-wide sc...1147 days ago
2202 days ago
Genome Assembly Tools and Software - PART2 !!
...framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. I...m is the only platform for standardising transcriptome projects: go from raw trace files to an annotated G...2736 days ago
Awesome perl frameworks, libraries and software - PART 2
...nbsp;- Declarative constraint-based structured drawing system in Perl (as per cha...m - Perl CPAN module Makefile::GraphViz - Draw building flowcharts from Make...erl - Perl library for SHODAN zzengineer/crawlpl - compact crawling to...2545 days ago
3998 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...g SNPs without a reference sequence. Ratan et al, BMC Bioinformatics 11:130, 2010 PubMedCentral Microindel detection in short-read sequence data. Krawitz et al, Bioinformatics 26(6...3830 days ago
3940 days ago
Webinar on Fast and Accurate DNA Variant Calling on 26 Apr 2017
Continuing our DNA-Seq webinar series, we'll present Strand NGS v3.0 best-practices: a workflow that identifies highly accurate variants from raw reads. Our best practices work...2622 days ago
3999 days ago
3694 days ago
Dr. Ken Buetow: IS & Personalized Medicine Lecture-Part 1
...and converting into actionable information. Currently, the context is drawn from fragmented research lit...rmation into the evidence necessary to support clinical care exceeds the raw human cognitive capacity. I...3921 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings; use strict; use Getopt::Long; use LWP::Simple; use URI::...2967 days ago
2177 days ago
Comment on "Short-read assembly using Spades !"
...eral steps for short-read assembly using SPAdes: Quality control of raw reads: Before running the assembly, it is important to ensure that the raw reads are of high quality and...466 days ago
Comment on "How to install Perl modules manually, using CPAN command, and other quick ways"
...ur macOS system. Install Homebrew if you haven't already installed it by entering the following command: /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebre...473 days ago