Question

How to extend contigs from single-end reads?

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2.7 years ago

A_heath ▴ 140

Hi all,

I have raw sequencing datas of metagenomes and all of them are single-end reads. I would want to prolong/extend contigs. I thought of PRICE (Ruby, JG., et al, 2013) but it only works with paired-end reads ... Do you have any recommendation on what software could I use?

Thank you for your much appreciated help in advance!

Have a great day

contigs contig extension single-end reads • 1.1k views

ADD COMMENT • link updated 2.7 years ago by shelkmike ▴ 920 • written 2.7 years ago by A_heath ▴ 140

score 4 · Accepted Answer · 2020-09-11

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2.7 years ago

GenoMax 129k

You can take a look at tadpole.sh from BBMap suite. A guide is available here.

ADD COMMENT • link 2.7 years ago by GenoMax 129k

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Thank you for your suggestion genomax!

ADD REPLY • link 2.7 years ago by A_heath ▴ 140

score 3 · Accepted Answer · 2020-09-11

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2.7 years ago

shelkmike ▴ 920

There are many such tools. For example:

ADD COMMENT • link 2.7 years ago by shelkmike ▴ 920

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Thank you so much shelkmike!

ADD REPLY • link 2.7 years ago by A_heath ▴ 140