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fqtools is a software suite for fast processing of FASTQ&n...arious file manipulations are supported. See below for a full list o...t file is specified, fqtools will attempt to read data from std...le or a pair of files will be generated. If no -o argument...2760 days ago
Standardized velvet assembly report
...ould be in your PATH) R (with Sweave) pdflatex (usually part of TeTeX) ggplot2 (from R prompt t...Perl Optional: BLAT or BLAST (to generate alignments against a referenc...rmute.sh to your liking, paying particular attention to the kmer, cvCut, expC...2759 days ago
- The objective of this activity is to help you understand how to run Velvet in general, how to accurately estimate the insert size of a paired-end library through the use of&nbs...
2759 days ago
- ...ling from the mapping result. PRISM is able to detect small insertions and abitra...discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-l...e found here. The authors may be contacted via e-mail at: prism at...
2757 days ago
- The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. EAGER encompasses both state-of-the-art tools for each ste...lored for ancient DNA data within a single integrated solution in an easily a...
2757 days ago
- Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput...ese trimming tasks by finding the adapter or primer sequences in an er...nces can contain IUPAC wildcard characters. Also, paired-end reads and...
2754 days ago
Understanding Greedy Algorithms
...s://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf http://schatzlab.cshl.edu/teaching/AssemblyClass/01.%20Ass...2756 days ago
- ...reads and contigs). The tool is written in Python 2.7. It also inclu...s to first map reads to contigs (instead of providing .sam files)....ed. These are .sam files produced after mapping reads to contigs and...read pair; -i) (Comma separated list of) insert size(s) of t...
2755 days ago
CISA: Contig Integrator for Sequence Assembly
...ever, no individual assembler guarantees the optimal assembly for di...e species. Optimizing various parameters in an assembler is often pe...In this study, we employ various state-of-the-art assemblers to gene...xisting tools. This tool is implemented in Python and requires MUMme...2753 days ago
BIMA V3: an aligner customized for mate pair library sequencing
Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural varia...d chromosomal abnormalities. Unfortunately, the mapping and alignment...n algorithm that is up to 20 times faster and 25% more accurate than p...2753 days ago
