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Old 02-04-2013, 01:38 AM   #14
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Location: Cambridge, UK

Join Date: Jul 2008
Posts: 146

I just noticed this thread, rather late.

There is CRAM from EBI, which has long term support and handles random access. It's the most direct competitor to BAM I would guess.

Alternatives are Goby (similar ratios, but even slower from my experience), Quip (faster encoding, great compression ratio, but no(?) random access) and SamComp1/2 (faster encoding, great compression ratio, no random access, and doesn't really implement the full SAM spec - more of a fastq compressor). Finally on that topic there are tools like quip again, fqzcomp and fastqz for compression of FASTQ data. [All 3 of these were SequenceSqueeze competition entries.]
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