Question

Aligning Contigs of various Mtb strains to a reference genome and get the variants

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6.3 years ago

Paul ▴ 80

Hi All,

I have a multiple of Mtb strains in the form of scaffolds.

Is there a way I can align these multiple scaffolds of multiple Mtb strains to a reference genome, to get a variant file with all the SNPs?

I know I can align reads to a reference genome and can get the variant file using samtools. But have no idea of aligning scaffolds or contigs to a reference genome to get all the variants with respect to the reference genome.

Assembly Mapping Variants GWAS • 2.5k views

ADD COMMENT • link updated 6.3 years ago by k.kathirvel93 ▴ 310 • written 6.3 years ago by Paul ▴ 80

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I think you can consider scaffolds as "Big reads"

ADD REPLY • link 6.3 years ago by Titus ▴ 910

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Is there such option in bowtie or bwa?

ADD REPLY • link 6.3 years ago by Paul ▴ 80

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Yes to me you just have to align it to a "classic" manner. Maybe you have to modify a bit the insertion score if you have big insertion due to the variability of your samples.

ADD REPLY • link 6.3 years ago by Titus ▴ 910

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But the format of reads are different from scaffolds, scaffolds are the string of sequences where as read files looks like this

AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEE/EEEEEEEEEEEEAEE<EEEEAEEEEEEAEAAEEAAEEEEEAEA/EEAEAAEA<<<AE<A<<
@NS500223:156:HWNKFBGXX:2:13204:6076:12546 1:N:0:TGACCAAT+AGATCTCG
CGCAGCGCCTTGGACAGGGCCAGGCAGTCGTCCATCGTCCGGAAGGCGTGCACGCCCTCGGGCAGCTCCCGGTCCGGGGTGAACAGGCCGCGCAGCGGCGGCAGGACGGGGTTGGAGCCGGTGGCCAGGACGAGCGTGTCGTATGCGATC
+
AAAAAEEEEEEEEEEAEEEEAEEEEEEEEEEEEAEEEEEEEEA/EEEEEEEEEEEEEEEEEEAEEEEEEEEEEA/EEEEEE/AEAEEEEEEEE/EEEE/EA</AEEEEEE<</EE/EAEEEEAA/<<EE/EE/AAEEE/6/A//A<</<6
@NS500223:156:HWNKFBGXX:2:13204:16689:12548 1:N:0:TGACCAAT+AGATCTCG
GAAGCCGACGGCGTAGAGCGCGAAGGCGACGACGACGGCGACCTGGCCGGCCGGGGAGCCGGTCATGCGTTCCAGGGCGCCGTCCTTCACCCCGTTCATGAGGAACAACGAGCCGACGCCGAGGACGGGGACGGCGTACGAGGTCATGCT

ADD REPLY • link 6.3 years ago by Paul ▴ 80

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You just ha to put your scaffold has fasta format , don't you think ?

ADD REPLY • link 6.3 years ago by Titus ▴ 910

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Thanks a lot it worked for me :) I aligned it using Bwa-mem and scanned it using freebayes

ADD REPLY • link 6.3 years ago by Paul ▴ 80

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@Titus, However, after the alignment I found that most of the SNPs are in the overlapping regions of the contigs. And these are contigs not scaffolds. Do I need to scaffold them before mapping or continue using contigs for the analysis?

ADD REPLY • link 6.3 years ago by Paul ▴ 80

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I'm not sure to understand it correctly, what do you mean by in the overlapping regions of the contigs ? Because you need an overlap to compare them :)

ADD REPLY • link 6.3 years ago by Titus ▴ 910

score 2 · Accepted Answer · 2018-08-20

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6.3 years ago

k.kathirvel93 ▴ 310

My Suggestion is, why can't you use mauve aligner? It is best to align and view and SNP extraction. You can align few many draft genomes with your reference genome in a single run. All the Best.

ADD COMMENT • link 6.3 years ago by k.kathirvel93 ▴ 310

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That's a good suggestion, but I have 200 MTb strains to align each with the reference genome.

ADD REPLY • link 6.3 years ago by Paul ▴ 80

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I think you can write for loop to take all the samples one by one in a order in a single run. I am sure we can go with 10 samples in mauve in a single run, so am asking you to read mauve manual carefully. All the Best.