REQUEST

REQUEST is a novel REad QUality Evaluation and Selection Tool (REQUEST) for evaluating the quality of third generation long reads.

License

Copyright (C) 2018 Hongdong Li (hongdong@csu.edu.cn), Wenjing Zhang (wjzhang@csu.edu.cn) School of Information Science and Engineering Central South University ChangSha CHINA, 410083

Environment

• REQUEST

git clone https://github.com/bioinfomaticsCSU/REQUEST.git
PATH=$PATH:/home/.../REQUEST
# if not set the PATH. You can move the raw data into the REQUEST.

• R
• Python 2.7+
• MECAT

git clone https://github.com/xiaochuanle/MECAT.git
cd MECAT
make 
cd 
PATH=$PATH:/home/.../MECAT/Linux-amd64/bin

Data processing

Input format

REQUEST is capable of processing FASTA files, which contains 2 lines to lines represent a read. You can download the test data: MAP006-PCR-1_2D_pass.fasta

For example:

>Reads_1
GCCATGCTTCCGTTTCAGTTACGTATTGCTGTGGAAGCTGTCGGACGA

If not, you can use fa2fa.py to convert the format. Usage:

python fa2fa.py input.fa output.fa

Input fa:
>Reads_1
TTACGTATTG
CTGTGGAAGC
CTTCAT
>Reads_2
TGCGTAAAAG
GAGGCGGTTT
GCGGTGGCG

Output fa:
>Reads_1
TTACGTATTGCTGTGGAAGCCTTCAT
>Reads_2
TGCGTAAAAGGAGGCGGTTTGCGGTGGCG

REQUEST pipeline

You can use REQUEST_main.sh .

sh REQUEST_main.sh input.fa task_name 

Output files

*.ft Each row represents the all 84 kinds of base rates and the length of a read.

*.fa.ft.sqscore the list of sqscores of the input fa_file.

*.score.sort.fa the reads with sqscores.

As follows:

# >Task_ID_sqscore
>test_out.6778_5.713
CATCCGTCACCGTCAGCGGTGCGTAAAAGGAGGCGGT
>test_out.9672_4.799
GCCATGCTTCCGTTTCAGTTACGTATTGCTGTGGAAGG
>test_out.8701_4.083
ACTCAGGCGCGATGACCGGT

If you don't want a sorted file. You can rewrite the last part of REQUEST_main.sh.

# sort 
paste $FQ.ft.sqscore $FQ.tab |sort -k1 -gr  > $FQ.score.sort.tab
python tab2fa.py  $FQ.score.sort.tab $task.score.sort.fa
rm  *.tab  $task.fa 
# no sort 
paste $FQ.ft.sqscore $FQ.tab  > $FQ.score.tab
python tab2fa.py  $FQ.score.tab $task.score.fa

Possible problems

• Segmentation fault This is generally because there are too many programs running at the same time, so you can change the "-t 100" into "-t 20" in the line 7 or 8 in the REQUEST_main.sh file.