This is a test version of Biostars. For the public version, visit https://www.biostars.org.
News: fastp 0.22 released, with new FASTQ deduplication feature.

fastp is a fast all-in-one preprocessing tool for FASTQ data. Now a new version v0.22.0 has been released, with a FASTQ deduplication feature.

Specify -D or --dedup to enable this option.

fastp
• 4,082 views • link
updated by Ram Ram • written by chen chen

Thanks for this program, it simplifies my life so much

• 0 views • link
written by ponganta ponganta

Hi,

I couldn't install the latest version from bioconda or with wget command, but I assume it was anaconda's bug; I managed to download it directly from the file section of github, so that was solved.

I couldn't use the deduplication function though, here was my command:

./fastp -i S672_L1_1.fq -o S672_L1_1.fp.fq -I S672_L1_2.fq -O S672_L1_2.fp.fq -D

and it returned this along with a 11Mb file compared to the 3.8Gb fastq file:

Killed

Hope you can look into this and point out if I did anything wrong or whatever led to this. Thanks.

• 0 views • link
updated by Ram Ram • written by Sang • Sang

If error says "killed" then your job likely ran out or memory. Deduplication (assuming fastp is doing it in memory) will need a lot of it.

Please post questions about tools in a separate thread. This post is for announcement of a new tool.

• 0 views • link
written by GenoMax GenoMax

charlie is there an option to de-dup using UMI information please?

• 0 views • link
written by samuel samuel

0 answers

No answers yet.

Log in to answer this question.

More posts like this