Useful Publications and Websites for Deep Sequencing Data Analysis
Global overview papers Next generation...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...3772 days ago
List of generic simulation software/tools/resource with brief description and homepage !!!
List of generic simulation software/tools/resource with brief...etaSim A tool to generate collections of synthetic reads that reflect the diverse taxo...t.ly/rlsim-gitpIRS Profile-based Illumina pair-end reads simulator https://code.google...3729 days ago
List of In-silico Binding Site Prediction Tools
Following are the list of In-silico Binding Site Prediction in Proteins tools CASTp : h...s channels, calculate pore dimensions and analyze atom accessibility. MolAxis reads files in the standard Protein...3736 days ago
Next generation sequencing in R or bioconductor environment
There are many R software and bioconductor packages for NGS d...is package is primairly focused on Solexa/Illumina reads. Documentation Rsamtools Rs...ns by modeling local concentrations of directional reads, and uses DNA fragment length...3617 days ago
Commercial and public next-gen-seq (NGS) software
Integrated solutions CLCbio Genomics Wor...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 @...3511 days ago
Software packages for next gen sequence analysis
Integrated solutions * CLCbio Genomics W...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...3235 days ago
2706 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
Commercial tools Strand NGS offers...tion to Sanger sequence data, reads from these high-throughput se...ats, users must also give raw reads in Fasta or Fastq Reference...tifies indels from paired-end reads Input: BAM (aligned in SAMto...n do single, de novo, somatic reads; requires that raw reads are...2901 days ago
Tools for Searching Repeats And Palindromic Sequences
What are genomic interspersed repeats? In the mid 1960's sci...e sequence 5' CGAAGC 3' that, when reversed, still reads CGAAGC. Palindromes are impo...CGAAGC 3', if inverted (reversed 180°), still reads CGAAGC. The European Molecul...2203 days ago
2861 days ago