Results for "split reads"
Top-level pages
"Bioinformatics is a science of biological predictions and analysis" -- Jitendra Narayan "The mathematical, s...enomes. Also the detection of gene fusion and gene fission (i.e, one protein is split...3936 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
Global overview papers Next genera...Compression of DNA sequence reads in FASTQ format. Deorowicz &a...FASTX-toolkit: FASTQ/A short-reads pre-processing tools Home Pag...n FM-index of the 1.2 billion reads] Readjoiner: a fast and memo...sis of the resulting sequence reads.] Genotyping by sequencing...3768 days ago
List of generic simulation software/tools/resource with brief description and homepage !!!
List of generic simulation software/tools/resource with b...MetaSim A tool to generate collections of synthetic reads that reflect the diverse taxo...it.ly/rlsim-gitpIRS Profile-based Illumina pair-end reads simulator https://code.google...3726 days ago
List of In-silico Binding Site Prediction Tools
...protein binding sites, we model the shape of a split pocket induced by a binding l...d to extract site-specific spatial patterns of split pockets as templates to match...nsions and analyze atom accessibility. MolAxis reads files in the standard Protein...3733 days ago
Perl one-liner for bioinformatician !!!
With the emergence of NGS technologies, and sequencing data most of the bioinformaticia...haracter longperl -le 'print join ", ", map { ord } split //, "hello world"'#Will print...tml http://bioexpressblog.wordpress.com/2013/04/05/split...3617 days ago
Next generation sequencing in R or bioconductor environment
...ackage is primairly focused on Solexa/Illumina reads. Documentation Rsamtools Rs...y modeling local concentrations of directional reads, and uses DNA fragment length...ovide this utility: ERANGE TopHat SpliceMap SplitSeek DNA-Methylation Data Ana...3613 days ago
Commercial and public next-gen-seq (NGS) software
Integrated solutions CLCbio Genomic...lter snps, do statistics for: reads, contigs and snps. Align/As...It quickly aligns millions of reads either with ungapped or gappe...ynamatix. Will align Illumina reads against a range of Refseq RNA...ification from Short Sequence Reads. BED file input. Raja Jothi @...3508 days ago
Software packages for next gen sequence analysis
Integrated solutions * CLCbio Genom...t aligns short DNA sequences (reads) to the human genome at a rat...It quickly aligns millions of reads either with ungapped or gappe...Assembles 20 - 64 bp Illumina reads to a FASTA reference genome....ut 20-25X coverage and paired reads. Developed by Daniel Zerbino...3231 days ago
- Reformat is a member of the BBMap/B...tool designed for converting reads or other nucleotide data betw...pling (to a fraction of input reads, or an exact number of reads...q out=y.fa Interleave paired reads: reformat.sh in1=x1.fq in2=x2...to/bbmap/current/ jgi.ReformatReads" for example, java -ea -Xmx20...
2703 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...ats, users must also give raw reads in Fasta or Fastq Reference...tifies indels from paired-end reads Input: BAM (aligned in SAMto...chine - predicts indels, uses split read alignment profiles, vali...n do single, de novo, somatic reads; requires that raw reads are...2898 days ago
