REAPR: a universal tool for genome assembly evaluation
...uracy of a genome assembly using mapped paired end reads, without th...used in any stage of an assembly pipeline to automatically break in...errors in an assembly for manual inspection. It reports mis-assembli...semblies. REAPR works best using mapped read pairs from a large inse...2998 days ago
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Trimmomatic: A flexible read trimming tool for Illumina NGS data
...nd: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz...unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING...INGWINDOW:4:15 MINLEN:36 This will perform the following: Remove...w, cutting when the average quality per base drops below 15 (SLIDING...2990 days ago
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HOMER: Software for motif discovery and next-gen sequencing analysis
This tutorial covers topics independently of HOMER, and represents knowledge which is important to know before diving head first into more advanced analysis tools such as HOMER....2979 days ago
mrFAST: Micro Read Fast Alignment Search Tool
mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery...ons. mrFAST maps short reads with respect to user defined error thres...e parameters and tune mrFAST with respect to the library settings. mr...2979 days ago
CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
...or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is a hierachical assembly pipeline which runs in four steps:...2962 days ago
Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
..., with an ideogramoutput architecture, where the patterns are represented with several HSV values (only value varies). The method can perform both in small- and large...2979 days ago