Hi there! Today, I would like to give some information and links about the tools used generally for sequence assembly, soon I am going to post a new article about the current state-of-the-art in visualization focusing on NGS.

AMOS is collection of tools and class interfaces for the assembly of DNA sequencing reads.
Bowtie is an ultrafast, memory-efficient short read aligner.
Cap3 is a DNA sequence assembly program.
Consed is a tool for viewing, editing, sequence assemblies created with phrap.
EagleView is an information-rich genome assembler viewer with data integration capability.
Gap5 is a general purpose multiple alignment program for DNA or proteins.
GigaBayes is a short-read SNP and short-INDEL discovery program.
Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines.
Maqview is graphical read alignment viewer.
MOSAIK is a suite comprising of three modular programs: MosaikBuild, MosaikAligner, and MosaikAssembler.
Phrap is a program for assembling shotgun DNA sequence data.
Phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.
PolyPhred is a program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions.
VAAL is a polymorphism discovery algorithm for short reads.
Velvet is a sequence assembler for very short reads.

Heidelberg varış sabah saat 8:44. Kayıtlar 9:00 ile 10:00 arasında. En önce kayıt yaptıranlardan biriydim. Kayıt yapan bayanlardan iki tanesi adımı söylemekte zorlandılar. Kayıt gerçekleşti, bavullar bırakıldı. Çay aldım kendime içiyorum. Elimde konferans programı bir yandan da onu gözden geçiyorum. Makale sayısı 10-15 olsun, 90 tanede poster var diyelim, ya da şöyle yapalım bu yazıyı şimdilik burda bırakıyorum.
Bugünde üçüncü gün, artık workshop bitti sayılır, biraz başım ağrıyor, yoruldum hatta. Novalgin aldım, bu ilacıda içme falan derler ama bana iyi geliyor diye geleneği devam ettiriyorum.