id	sid	tid	token	lemma	pos
0k225b01f48	1	1	genome	genome	NOUN
0k225b01f48	1	2	sequencing	sequence	VERB
0k225b01f48	1	3	technologies	technology	NOUN
0k225b01f48	1	4	have	have	AUX
0k225b01f48	1	5	revolutionized	revolutionize	VERB
0k225b01f48	1	6	biology	biology	NOUN
0k225b01f48	1	7	in	in	ADP
0k225b01f48	1	8	the	the	DET
0k225b01f48	1	9	past	past	ADJ
0k225b01f48	1	10	two	two	NUM
0k225b01f48	1	11	decades	decade	NOUN
0k225b01f48	1	12	,	,	PUNCT
0k225b01f48	1	13	yet	yet	CCONJ
0k225b01f48	1	14	data	data	NOUN
0k225b01f48	1	15	analysis	analysis	NOUN
0k225b01f48	1	16	has	have	AUX
0k225b01f48	1	17	lagged	lag	VERB
0k225b01f48	1	18	behind	behind	ADP
0k225b01f48	1	19	data	datum	NOUN
0k225b01f48	1	20	production	production	NOUN
0k225b01f48	1	21	.	.	PUNCT
0k225b01f48	2	1	in	in	ADP
0k225b01f48	2	2	this	this	DET
0k225b01f48	2	3	thesis	thesis	NOUN
0k225b01f48	2	4	,	,	PUNCT
0k225b01f48	2	5	we	we	PRON
0k225b01f48	2	6	present	present	VERB
0k225b01f48	2	7	a	a	DET
0k225b01f48	2	8	framework	framework	NOUN
0k225b01f48	2	9	for	for	ADP
0k225b01f48	2	10	analyzing	analyze	VERB
0k225b01f48	2	11	genomic	genomic	ADJ
0k225b01f48	2	12	data	datum	NOUN
0k225b01f48	2	13	in	in	ADP
0k225b01f48	2	14	more	more	ADV
0k225b01f48	2	15	flexible	flexible	ADJ
0k225b01f48	2	16	ways	way	NOUN
0k225b01f48	2	17	than	than	ADP
0k225b01f48	2	18	previous	previous	ADJ
0k225b01f48	2	19	techniques	technique	NOUN
0k225b01f48	2	20	.	.	PUNCT
0k225b01f48	3	1	first	first	ADV
0k225b01f48	3	2	,	,	PUNCT
0k225b01f48	3	3	the	the	DET
0k225b01f48	3	4	framework	framework	NOUN
0k225b01f48	3	5	allows	allow	VERB
0k225b01f48	3	6	researchers	researcher	NOUN
0k225b01f48	3	7	to	to	PART
0k225b01f48	3	8	design	design	VERB
0k225b01f48	3	9	analyses	analysis	NOUN
0k225b01f48	3	10	that	that	PRON
0k225b01f48	3	11	compare	compare	VERB
0k225b01f48	3	12	genomic	genomic	ADJ
0k225b01f48	3	13	samples	sample	NOUN
0k225b01f48	3	14	directly	directly	ADV
0k225b01f48	3	15	instead	instead	ADV
0k225b01f48	3	16	of	of	ADP
0k225b01f48	3	17	relying	rely	VERB
0k225b01f48	3	18	on	on	ADP
0k225b01f48	3	19	reference	reference	NOUN
0k225b01f48	3	20	-	-	PUNCT
0k225b01f48	3	21	relative	relative	ADJ
0k225b01f48	3	22	variant	variant	NOUN
0k225b01f48	3	23	calls	call	VERB
0k225b01f48	3	24	,	,	PUNCT
0k225b01f48	3	25	as	as	SCONJ
0k225b01f48	3	26	most	most	ADJ
0k225b01f48	3	27	current	current	ADJ
0k225b01f48	3	28	tools	tool	NOUN
0k225b01f48	3	29	do	do	VERB
0k225b01f48	3	30	.	.	PUNCT
0k225b01f48	4	1	second	second	ADV
0k225b01f48	4	2	,	,	PUNCT
0k225b01f48	4	3	we	we	PRON
0k225b01f48	4	4	provide	provide	VERB
0k225b01f48	4	5	utilities	utility	NOUN
0k225b01f48	4	6	to	to	PART
0k225b01f48	4	7	look	look	VERB
0k225b01f48	4	8	at	at	ADP
0k225b01f48	4	9	both	both	DET
0k225b01f48	4	10	assembly	assembly	NOUN
0k225b01f48	4	11	data	datum	NOUN
0k225b01f48	4	12	and	and	CCONJ
0k225b01f48	4	13	resequencing	resequence	VERB
0k225b01f48	4	14	data	datum	NOUN
0k225b01f48	4	15	in	in	ADP
0k225b01f48	4	16	the	the	DET
0k225b01f48	4	17	same	same	ADJ
0k225b01f48	4	18	analysis	analysis	NOUN
0k225b01f48	4	19	,	,	PUNCT
0k225b01f48	4	20	where	where	SCONJ
0k225b01f48	4	21	previous	previous	ADJ
0k225b01f48	4	22	tools	tool	NOUN
0k225b01f48	4	23	were	be	AUX
0k225b01f48	4	24	restricted	restrict	VERB
0k225b01f48	4	25	to	to	ADP
0k225b01f48	4	26	either	either	CCONJ
0k225b01f48	4	27	looking	look	VERB
0k225b01f48	4	28	at	at	ADP
0k225b01f48	4	29	an	an	DET
0k225b01f48	4	30	assembly	assembly	NOUN
0k225b01f48	4	31	or	or	CCONJ
0k225b01f48	4	32	at	at	ADP
0k225b01f48	4	33	resequencing	resequence	VERB
0k225b01f48	4	34	data	datum	NOUN
0k225b01f48	4	35	.	.	PUNCT
0k225b01f48	5	1	finally	finally	ADV
0k225b01f48	5	2	,	,	PUNCT
0k225b01f48	5	3	our	our	PRON
0k225b01f48	5	4	framework	framework	NOUN
0k225b01f48	5	5	allows	allow	VERB
0k225b01f48	5	6	researchers	researcher	NOUN
0k225b01f48	5	7	to	to	PART
0k225b01f48	5	8	flexibly	flexibly	ADV
0k225b01f48	5	9	incorporate	incorporate	VERB
0k225b01f48	5	10	alignments	alignment	NOUN
0k225b01f48	5	11	to	to	ADP
0k225b01f48	5	12	arbitrarily	arbitrarily	ADV
0k225b01f48	5	13	many	many	ADJ
0k225b01f48	5	14	reference	reference	NOUN
0k225b01f48	5	15	sequences	sequence	NOUN
0k225b01f48	5	16	into	into	ADP
0k225b01f48	5	17	their	their	PRON
0k225b01f48	5	18	analysis	analysis	NOUN
0k225b01f48	5	19	.	.	PUNCT
0k225b01f48	6	1	we	we	PRON
0k225b01f48	6	2	describe	describe	VERB
0k225b01f48	6	3	flexreseq	flexreseq	PROPN
0k225b01f48	6	4	,	,	PUNCT
0k225b01f48	6	5	the	the	DET
0k225b01f48	6	6	software	software	NOUN
0k225b01f48	6	7	implementation	implementation	NOUN
0k225b01f48	6	8	of	of	ADP
0k225b01f48	6	9	this	this	DET
0k225b01f48	6	10	framework	framework	NOUN
0k225b01f48	6	11	.	.	PUNCT
0k225b01f48	7	1	flexreseq	flexreseq	PROPN
0k225b01f48	7	2	allows	allow	VERB
0k225b01f48	7	3	researchers	researcher	NOUN
0k225b01f48	7	4	to	to	PART
0k225b01f48	7	5	easily	easily	ADV
0k225b01f48	7	6	customize	customize	VERB
0k225b01f48	7	7	resequencing	resequence	VERB
0k225b01f48	7	8	analyses	analysis	NOUN
0k225b01f48	7	9	using	use	VERB
0k225b01f48	7	10	a	a	DET
0k225b01f48	7	11	simple	simple	ADJ
0k225b01f48	7	12	configuration	configuration	NOUN
0k225b01f48	7	13	file	file	NOUN
0k225b01f48	7	14	to	to	PART
0k225b01f48	7	15	define	define	VERB
0k225b01f48	7	16	positions	position	NOUN
0k225b01f48	7	17	of	of	ADP
0k225b01f48	7	18	interest	interest	NOUN
0k225b01f48	7	19	.	.	PUNCT
0k225b01f48	8	1	we	we	PRON
0k225b01f48	8	2	give	give	VERB
0k225b01f48	8	3	results	result	NOUN
0k225b01f48	8	4	from	from	ADP
0k225b01f48	8	5	applications	application	NOUN
0k225b01f48	8	6	of	of	ADP
0k225b01f48	8	7	these	these	DET
0k225b01f48	8	8	tools	tool	NOUN
0k225b01f48	8	9	such	such	ADJ
0k225b01f48	8	10	as	as	ADP
0k225b01f48	8	11	genotyping	genotype	VERB
0k225b01f48	8	12	strains	strain	NOUN
0k225b01f48	8	13	of	of	ADP
0k225b01f48	8	14	plasmodium	plasmodium	NOUN
0k225b01f48	8	15	falciparum	falciparum	NOUN
0k225b01f48	8	16	,	,	PUNCT
0k225b01f48	8	17	finding	find	VERB
0k225b01f48	8	18	diversity	diversity	NOUN
0k225b01f48	8	19	and	and	CCONJ
0k225b01f48	8	20	divergence	divergence	NOUN
0k225b01f48	8	21	between	between	ADP
0k225b01f48	8	22	strains	strain	NOUN
0k225b01f48	8	23	of	of	ADP
0k225b01f48	8	24	anopheles	anophele	NOUN
0k225b01f48	8	25	gambiae	gambiae	NOUN
0k225b01f48	8	26	,	,	PUNCT
0k225b01f48	8	27	detecting	detect	VERB
0k225b01f48	8	28	inversions	inversion	NOUN
0k225b01f48	8	29	based	base	VERB
0k225b01f48	8	30	on	on	ADP
0k225b01f48	8	31	assembly	assembly	NOUN
0k225b01f48	8	32	and	and	CCONJ
0k225b01f48	8	33	alignment	alignment	NOUN
0k225b01f48	8	34	information	information	NOUN
0k225b01f48	8	35	from	from	ADP
0k225b01f48	8	36	a.	a.	NOUN
0k225b01f48	8	37	gambiae	gambiae	NOUN
0k225b01f48	8	38	,	,	PUNCT
0k225b01f48	8	39	and	and	CCONJ
0k225b01f48	8	40	exploring	explore	VERB
0k225b01f48	8	41	resequencing	resequence	VERB
0k225b01f48	8	42	analysis	analysis	NOUN
0k225b01f48	8	43	using	use	VERB
0k225b01f48	8	44	alignments	alignment	NOUN
0k225b01f48	8	45	to	to	ADP
0k225b01f48	8	46	multiple	multiple	ADJ
0k225b01f48	8	47	reference	reference	NOUN
0k225b01f48	8	48	sequences	sequence	NOUN
0k225b01f48	8	49	.	.	PUNCT