| Version 9 (modified by bonnalraoul, 16 years ago) |
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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
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
Assemble tools
Velvet
EMBOSS
