Compression ratio and genome assembly quality

#!/bin/bash -e in=$1 f2b=$in.f2b bzi=$in.bzi rm -f $f2b $bzi mkfifo $f2b $bzi faToTwoBit $in $f2b & tee $bzi < $f2b | perl -ne '$t+=length($_); END{print "$t\n"}' > $in.bsz & comp=`bzip2 < $bzi | perl -ne '$t+=length($_); END{print "$t\n"}'` wait perl -ne "printf qq{%.4f\n}, 100*$comp/\$_" $in.bsz rm -f $f2b $bzi $in.bsz

Compression ratio and genome assembly quality
Posted 7:20 AM

When doing genomic assembly, you would expect the complexity of the completed genome to be comparable to the complexity of genomes of similar size and neighboring taxonomy.

One easy measure of complexity is the degree to which a genome can be compressed. After converting to 2-bit format, some genomes compress better than others. bzip2 has a large default block size and the ratio of compressed vs uncompressed size of a 2-bit fasta should result in a good measure of complexity.

Can't think of a good source of data to test this theory. Maybe look at the Amos validate paper.

Source of "complexity-measure.sh" works well... fast, and produces a percentage as its only output:

#!/bin/bash -e

in=$1

f2b=$in.f2b
bzi=$in.bzi

rm -f $f2b $bzi

mkfifo $f2b $bzi

faToTwoBit $in $f2b &

tee $bzi < $f2b | perl -ne '$t+=length($_); END{print "$t\n"}' > $in.bsz &
comp=`bzip2 < $bzi | perl -ne '$t+=length($_); END{print "$t\n"}'`
wait

perl -ne "printf qq{%.4f\n}, 100*$comp/\$_" $in.bsz

rm -f $f2b $bzi $in.bsz

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