Assemblathon 2 ‘bird’ Stats

Here are the basic assembly stats for the bird data: contig cutoff size=250bp

	N:250	n:N50	N80	N50	N20	max	sum	name
Average	105054.3	8628.2	1235754.8	3899483.5	9540090.4	19342630.9	1.03E+09
	849	57	2283	8580	20266	51162	1933317	bird_8C_contigs.fa
	826	47	2930	11620	23347	57581	2026432	bird_8C_scaffolds.fa
	70467	7137	15629	39414	87076	554547	1.04E+009	bird_6C_contigs.fa
	16495	32	3207491	10011138	19098421	49826764	1.04E+009	bird_6C_scaffolds.fa
	37670	4312	25386	67833	146481	671540	1.06E+009	bird_7C_contigs.fa
	8062	23	2481996	10935449	37556899	50983430	1.06E+009	bird_7C_scaffolds.fa
	190778	16265	6158	18177	38632	235482	1.07E+009	bird_10C_contigs.fa
	92853	81	228034	2965671	8717439	32814605	1.07E+009	bird_10C_scaffolds.fa
	54037	4855	18956	56996	141343	712654	1.10E+009	bird_11C_contigs.fa
	4341	18	1833827	16806221	42927674	64643934	1.10E+009	bird_11C_scaffolds.fa
	65217	5939	21833	53463	107654	666240	1.11E+009	bird_13E_contigs.fa
	10697	23	6275406	14199076	31408994	65236555	1.11E+009	bird_13E_scaffolds.fa
	66411	6094	20919	52129	105709	500974	1.11E+009	bird_14E_contigs.fa
	10685	23	6278647	14202455	31417212	65264275	1.11E+009	bird_14E_scaffolds.fa
	92575	7505	13282	39267	88316	666240	1.11E+009	bird_12C_contigs.fa
	10703	23	6286291	14221761	31447220	65359764	1.11E+009	bird_12C_scaffolds.fa
	75487	8235	16695	41221	80970	465622	1.17E+009	bird_4C_contigs.fa
	34104	638	157708	516390	1104665	2942284	1.17E+009	bird_4C_scaffolds.fa
	88197	2156	32923	134986	342996	1818605	1.17E+009	bird_3E_contigs.fa
	41941	22	4805477	14768158	35825618	67706724	1.17E+009	bird_3E_scaffolds.fa
	84487	1383	40265	193162	559349	2740960	1.17E+009	bird_2C_contigs.fa
	41941	22	4815185	14777158	35841802	67755865	1.17E+009	bird_2C_scaffolds.fa
	77515	3165	31975	102941	220703	849043	1.19E+009	bird_9C_contigs.fa
	54666	177	405855	1746932	4194166	11487706	1.19E+009	bird_9C_scaffolds.fa
	346930	5356	4039	50966	170544	1468602	1.31E+009	bird_1C_contigs.fa
	293817	270	17136	894118	4140394	19295806	1.31E+009	bird_1C_scaffolds.fa
	175676	21521	10126	23871	50265	424718	1.84E+009	bird_5C_contigs.fa
	130759	7527	13236	38683	323074	4670483	1.84E+009	bird_5C_scaffolds.fa
	486721	77970	1478	3334	7742	203381	9.98E+006	bird_15C_contigs.fa
	486721	77970	1478	3334	7742	203381	9.98E+006	bird_15C_scaffolds.fa

dan

Hi Matt, thanks for posting this. It looks like you have reported the scaffold stats in a way that ignores the captured gaps/runs of N’s within scaffolds. If its not too much of an imposition it would be useful to see the scaffold numbers (or even just the total scaffold lengths) including these gaps, which presumably represent sequences that are linked across but whose sequence is unknown (or found in erroneously unlinked short scaffolds).