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Table 1 Summary of sequencing libraries as input to the ALLPATHS-LG assembler

From: An improved genome release (version Mt4.0) for the model legume Medicago truncatula

Type Library name Library size # of reads Sequence coverage (X-fold) # of pairs Pair coverage (X)
Frag Illumina PE-200 207 ± 40 212,635,636 49.5 84,508,836 57.9
Frag Illumina PE-376 244 ± 75 269,583,440 48.3 87,087,424 73.1
Frag total   482,219,076 97.8 171,596,260 131.1
Jump Illumina 3Kb 2014 ± 785 117,669,776 13.2 19,112,272 34
Jump Illumina 4.5Kb 4866 ± 549 78,918,228 7.3 6,426,863 104.2
Jump Illumina 5Kb 5062 ± 776 200,273,082 32.5 9,097,003 154.9
Jump Illumina 7Kb 7455 ± 998 50,076,448 0.8 424,740 10.8
Jump 454 FLX 3Kb 2260 ± 816 1,499,510 0.4 440,037 3.7
Jump total   448,437,044 54.2 35,500,915 307.7
Long_jump Fosmid lib 35000 ± 7000 68,372 0 7,626 0.8
Long_jump BAC lib mtrs 65000 ± 13000 40,080 0 9,269 1.9
Long_jump BAC libs mte1 and mth2 100000 ± 20000 151,538 0 38,306 14.5
Long_jump BAC lib mth4 200000 ± 40000 17,042 0 4,303 2.7
Long_jump Total   277,032 0.1 59,504 19.9
  1. Type refers to the ALLPATHS terminology of sequencing libraries - “frag” refers to short insert paired-end libraries that are typically two ends of <1Kb fragments, “jump” refers to long insert mate pair libraries that are typically between 1Kb to 10Kb, “long_jump” refers to the ends of fosmids and BACs.