Satellite meeting for Sequence analysis tools from the next generation sequencer ¶

Topics ¶

To share our knowledges about sequence analysis tools. Please write what you know about the tools.

Also see  Bioinformatics for Next Generation Sequencing virtual issue -- yaskaz@ddbj (thanks to ichan) and  Table 3 of Jay Shendure & Hanlee Ji., Next-generation DNA sequencing, Nature Biotech. (thanks to hinaichigo)

Mapping tools ¶

• Maq
• ELAND
•  BOWTIE Ultra-short reads, Burrows-Wheeler index.
•  Lasergene Support 454/Solexa. GUI interface for displaying alignments and contigs organization (scaffolds)
•  GSMapper
  • Map reads to any reference genome and generate a consensus sequence.
  • Easily view all differences compared to the reference sequence with automatic output to separate files: Insertions (blocks up to 50 bases), Deletions (blocks up to 50 bases), SNPs
  • Quickly identify high confidence difference compared to the reference genome, which are singled out in a separate file.
  • Compare large, complex genomes of any size including: resequencing of whole genomes from humans, plants, yeasts, bacteria, fungi, viruses, YACs, BACs, fosmids
  • Data outputs: fna.file (sequence of contigs, FASTA format), qual.file (corresponding Phred equivalent quality score), ace.file (consensus alignment of the reads against a given reference sequence)

•  SHRiMP supports letter-space (454/Solexa), color-space (Solid) and Helicos 2-pass space. Spaced-seeds followed by S-W.
•  Lastz Blast(z) variant. Has parameter settings tuned for 454 and Solexa mapping for both reference based assembly and variant discovery.
•  EMBOSS tools for NGS
•  LAST

many mores.... but never used.

Assemble tools ¶

•  GSAssembly
  • Performs whole genome shotgun assembly of genomes with or without paired-end data.
  • Order contigs into scaffolds using supported paired-end reads.
  • Assemble larger, more complex genomes up to 400 megabases in size with a 64-bit assembler or up to 20 megabases with a 32-bit assembler.
  • Co-assemble with Sanger Sequencing reads.
  • Select the read files you want to assemble by browsing in the GUI.
  • Data outputs: fna.file (sequence of contigs, FASTA format), qual.file (corresponding Phred equivalent quality score), ace.file (alignment of the reads to contig sequence)

•  Lasergene Support 454/Solexa. GUI interface for displaying alignments and contigs organization (scaffolds)
•  Velvet
•  EMBOSS tools for NGS

many mores.... but never used.

Platforms ¶

•  Roche, 454
•  Illumina, Solexa
•  AB, Solid

Notes ¶

• Every new software must handle this "huge" amount of data.
• Some veriations SNP, deletion, insertion can by identified during mapping/assembly process, other things more "new biology" needs more work by bionformaticians.
• Support from biologists is required in order to discover more new things.

TODOs ¶

Connected to SatelliteBigData a LIMS infrastructure is suggested for tracking history and infer problems coming from wet-lab.

From SatelliteVisualization these tools could be very usefull to explore at any level all the informations collected, from the alignment (lower) up to annotation/comparison (higher). The informations are intended as local (faltfile/databases/webservices) or remote (databases/webservices).

Editing in real time, providing alternatives for hypothesis.

Easy tools to integrate informations coming from different platforms (illumina, 454, solid).