IDBA Assembly Help

Question

[vanessaarfer]

For the IDBA-UD assembly, is it necessary to use fasta files or How can I enter fastq files?

I have tried to get your manual but I can not find information.

Help, please!!

Answer 1

[lyx694214251]

there is a script named 'fq2fa' that can merge two fastq files and convert them into fasta format

Answer 2

[m.m]

For future users: the script mentioned by @lyx694214251 is included in the idba-ud package and is called "fq2fa" and can be found in the bin folder of the package (g.e. "~/idba/bin/fq2fa).

For paired reads saved in two seperate files (and assuming the reads are ordered), the command is:

bin/fq2fa --merge --filter read_1.fq read_2.fq read.fa

Or to convert a single FASTQ file to FASTA via:

bin/fq2fa --paired --filter read.fq read.fa

More information is available on the developer's github: https://github.com/loneknightpy/idba