• bedtools - Project Hosting on Google Code
  "The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage."
  in Public bookmarks with bioinformatics freeware genetics genomics sequencing
• European Nucleotide Archive Reads | EBI
  "The European Nucleotide Archive accepts data generated by next-generation sequencing methodologies such 454, Illumina and ABI SOLiD. This is a new service that will provide utility for those generating and using data for such applications as genome assembly, re-sequencing for polymorphism analysis, gene expression, epigenomics and others. The data will be deposited in the European Read Archive (ERA) which works in close collaboration with the NCBI Short Read Archive (SRA). An ERA submission consists of trace data files and XML meta-data files. ERA uses the same XML meta-data formats as SRA."
  in Public bookmarks with bioinformatics sequencing
• FASTQ Format
  "FASTQ format stores sequences and Phred qualities in a single file."
  in Public bookmarks with sequencing standards
• HLA caller algorithm - GSA
  "... generic algorithm to call HLA alleles at 4-digit resolution from next-generation sequence data"
  in Public bookmarks with bioinformatics genomics nextgen sequencing
• MINSEQE - Workgroups - MGED
  in Public bookmarks with bioinformatics sequencing standards

sequencing from all users