next-generation sequencing analysis method——paper2

Here, we outline some of the tools and databases commonly used for the analysis of next-generation sequence data with comment on their utility.

GENOME ASSEMBLYALGORITHMS

（1）SSAKE: one of the first short-read assemblers released (does not incorporate data from paired reads and thus has no way to identify and differentiate between repetitive regions).
（2）VCAKE: does not make use of paired read data and so also cannot resolve ambiguities caused by repetitive regions.
…

MAPPING READS TO A REFERENCE

tools: BLAST, MAQ, Bowtie, SOAPaligner/SOAP2, BWA and BFAST
（1）BLAST: BLAT is used for rapid sequence-based searching in a number of public genome browsers and genome
repositories, including The UCSC Genome Browser Database and EnsEMBL
（2）MAQ: mapping tens of millions of short reads to a reference genome efficiently and dealing with the major issue of alignment accuracy; ungapped alignment on single reads but is capable of making use of read pair information and Phred base quality of the read to calculate the error probability of a read aligning to a position
（3）BFAST: slower than other popular aligners such as Bowtie, BWA and MAQ but faster than BLAST and with lower reported false-mapping rates overall. This full gapped local alignment allows BFAST to handle SNPs, insertion and/or deletions better than the other aligners.
（4）Bowtie: Burrows–Wheeler indexing for the rapid alignment of short nucleotide sequences to genomic sequence. Permit sequence mismatches and is able to be run on multiple CPU cores simultaneously.
Reciprocal support for a variety of other short-read applications, including Samtools,
Forms the basis of the RNA-seq alignment tool, Tophat, and the related expression analysis software package, Cufflinks
（5）SOAP2: Burrows–Wheeler indexing; up to two mismatches in its sequence alignment and has support for paired-read data; align reads faster than Bowtie; less comprehensive results;
（6）BWA: Burrows–Wheeler based short read alignment tool to support gapped alignment of short reads;
The support for gapped alignment becomes of greater relevance as sequencing read lengths increase and are more likely to contain indels when aligned to divergent genomes and sequences
（7）SHRiMP: a set of algorithms and methods to map short reads against a target genome, even in the presence of a large amount of polymorphism.
This package has been updated to SHRiMP2 which supports more formats, such as Fasta and Fastq input, SAM output, Illumina/Solexa, Roche/454 and AB/SOLiD reads, and supports paired read mapping, miRNA mapping and parallel computation

NEXT-GENERATION TRANSCRIPTOMICS

TopHat： An open-source software designed to align reads from RNA-Seq to a reference genome without relying on known splice sites.
TopHat takes a reference genome (as a Bowtie index) and RNA-Seq reads as FASTA or FASTQ and produces alignments in SAM format.

TopHat is implemented in C⁺⁺ and runs on Linux and Mac OS X. It uses the SeqAn library and requires Bowtie and MAQ

Cufflinks assembler: can identify complete novel transcripts and probabilistically assign reads to isoforms. Additionally it contains Cuffcompare and Cuffdiff tools.

Cuffcompare: validates Cufflinks output, transfrags (assembled transcript fragments), against annotated
transcriptomes and also finds transfrags common to multiple assemblies.

**Cuffdiff **: differential expression testing.
This assembler was designed to investigate transcriptional, splicing regulation and find the minimal number of transcripts that ‘explain’ the reads (that is, every read should be contained in some transcript).

VISUALIZATION TOOLS

Bambino ==
BAM formatted input data files; pool data within the programme; analysis of variation between samples; annotation of UCSC genome annotations on the given contig

Tablet
ACE, AFG, MAQ, SOAP, SAM and BAM; provides a contig overview as well as a sequence level viewer; import feature annotations in the form of GFF files

Integrative Genomics Viewer (IGV)
http://www.broadinstitute.org/igv/
array-based data, such as expression and copy-number arrays, RNA interference screens, gene expression, methylation and genomic annotations.
== Savant (Sequence Annotation, Visualization and ANalysis Tool) Genome Browser
FASTA, BED, SAM/BAM, WIG, GFF and any tab-delimited text file containing positional annotations
MagicViewer
short-read alignment visualization and annotation; requires
a reference genome sequence in fasta format, a sorted BAM file containing the aligned short reads and an optional reference genome annotation file in GFF format.
allows users to adjust parameters (primer length, Tm, GC content, product Tm and the number of primers) for Primer3 in order to amplify a specific genomic region.
Geneious