NGSFormatConverter Manual

Version 1.0

Bairong Shen,Wentao Wu

March 26,2012

Contents

1.Introduction to NGSFormatConverter

1.1 What can you do with NGSFormatConverter

1.2 System requirements

2.Quick start to use NGSFormatConverter

2.1 Use NGSFC in command line

2.1.1 Synopsis

2.1.2 Commands and options

2.2 Use the GUI of NGSFC

2.2.1 Overview

2.2.2 Conversion by build-in scripts

2.2.3 Use external scripts

2.2.4 Retrieve databases

Appendix A Conversion type

Appendix B Output naming rules

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1.Introduction to NGSFormatConverter

1.1 What can you do with NGSFormatConverter

NGSFormatConverter(NGSFC)is first designed for format conversion and database retrieval of

deep sequencing. But I found many excellent softwares of deep sequencing are not easy to use.

For example,many softwares can be described as "one command,one file", if there are a lot of

files to process, it is very troublesome. So the NGSFC can call other programs and scripts to process

a list of files. I hope researchers would consider it to be useful.

The NGSFC has these functions in brief:

1. Format conversion,and also can load external scripts

2. Batch processing

3. Execute other programs with batch processing

4. Databases retrieval and also can add new databases

1.2 System requirements

NGSFC will run on most platforms with the Java 7 or above installed.

2.Quick start to use NGSFormatConverter

2.1 Use NGSFC in command line

2.1.1 Synopsis

Java -jar NGSFC.jar -i <input> -o <output> [-s <script>] -t <type> [arguments]

The order of arguments is not mandatory,but the arguments must be in pair(e.x <-i> <input>).And the rest will be recognized as [arguments].

Java -jar NGSFC.jar -c <configfile>

All the information is in the config file.For more information,please refer to config file example.

Java -jar NGSFC.jar -h

Show help.

2.1.2 Commands and options

-i

Input file.

-o

Output directory.

-s

Script file if use external scripts.

-t

Use the build-in scripts to convert.if use external scripts use 10000. For more infomation of the conversion_type , please see Appendix A.

-c

Config file.In field inputs and args,use ;(semicolon) to separate multiple inputs.To use script,type must be 10000.

Example:

inputs = 1.fq;2.fq #multiple inputs must be separated by semicolon

output = outputs #give the output directory path

script = gtf2gff3.pl #if use external script,write the script file path

type = -fq2fa #conversion type,for more information,please refer to Appendix A.Write 10000 if use external script.

args = arg1;arg2 #arguments for conversion,use semicolon to separate.

-h

Show help.

2.2 Use the GUI of NGSFC

2.2.1 Overview

Fig.1. Overview of NGSFormatConverter

2.2.2 Conversion by build-in scripts

Fig.2. Use build-in scripts

Step 1: Select Build-in Script tab.

Step 2: Select the input format in the list.

Step 3: Select the output format in the list.

Step 4: Add the files you want to process.

Step 5: Select the output directory.NGSFC will name the output file automatically. For more information please refer to Appeddix B.

Step 6: Input parameters if required.

Step 7: Press the start button and have a coffee,it will done soon.

2.2.3 Use external scripts

If NGSFC doesn't have the conversion scripts you want or you want to execute a program(for example a analysis program), follow the following steps.

Step 1: Select Custom Scripts tab.

Step 2: Select the script or program in the list(NGSFC will load all the scripts(pl,py,exe,jar...) in the scripts directory.

Note:If you want to execute a perl script,you must have a perl interpreter installed.Other scripts is similar.

Step 3: The same as step 4 to step 7 above.

2.2.4 Retrieve databases

Fig.4. Database retrieval

To retrieve databases, follow the following steps.

Step 1: Select the databases you want to retrieve.

Step 2: Input your key words.

Step 3: Press Search button.

If you want to add some new databases,please do as follows.

Step 1: Press Edit button.

Step 2: Select a database if you want to modify or do not select anything if you want to add new.

Step 3: Input a name and URL.

Step 4: Press addnew button.

Note:The URL can not contain the key words.For example,if you want to search pubmed,you will input "http://www.ncbi.nlm.nih.gov/pubmed/?term=".

Appendix A :Conversion type

-fa2fq

FASTA to FASTQ.

The qual file must have the same file name with the fasta file and suffix ".qual". And in the same directory with fasta file.

-fa2fa

CSFASTA to FASTA.

-fa22bit

FASTA to 2bit.

-fq2fa

FASTQ to FASTA.

-fq2fq

Change FASTQ quality score. 0 for Sanger, 1 for Solexa, 2 for Illumina 1.3-1.4, 3 for Illumina 1.5+.

Arguments	Description
Input score	Input file quality score,required.
Output score	Output file quality score,required.

-fq2sm

FASTQ to SAM, more information please refer to Picard(http://picard.sourceforge.net/command-line-overview.shtml#FastqToSam).

Arguments	Description
FASTQ2	Input fastq file (optionally gzipped)for the second read of paired end data. Default value: null.
Quality format	Quality score format,sanger,solexa,Illumina 1.3+ or Illumina 1.5+,default value:sanger.
Read group name	Read group name Default value:A.
Sample name	Sample name to insert into the read group header.Default value:SampleName.
Library name	The library name to place into the LB attribute in the read group header Default value:null.
Platform unit	The platform unit (often run_barcode.lane ) to insert into the read group header Default value: null.
Platform	The platform type (e.g.illumina,solid)to insert into the read group header Default value: null.
Sequence center	The sequencing center from which the data originated. Default value: null.
Predicted insert size	Predicted median insert size, to insert into the read group header.Default value: null.
Description	Inserted into the read group header. Default value: null.

-qseq2fq

Qseq to FASTQ.

-qseq2fa

Qseq to FASTA.

-sc2fq

SCARF to FASTQ.

-sc2fa

SCARF to FASTA.

-2bit2fa

2bit to FASTA.

Arguments	Description
In one file	Put all the sequences in one FASTA file or in separated files.Default value:false.

-sm2bm

SAM to BAM.

-sm2fa

SAM to FASTA.

Arguments	Description
Second end FASTA	Output fasta file (if paired, second end of the pair fasta).Default value:null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
Output per read group	Output a fastq file per read group (two fastq files per read group if the group is paired). Default value: false. Possible values: {true, false} Cannot be used in conjuction with option(s) SECOND_END_FASTQ (F2) FASTQ (F)
Re-reverser	Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq Default value: true. Possible values: {true, false}
Include non-PF reads	Include non-PF reads from the SAM file into the output FASTQ files. Default value: false. Possible values: {true, false}
Clipping attrbutes	The attribute that stores the position at which the SAM record should be clipped Default value: null.
Clipping action	The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Default value: null.
Read1 trim	The number of bases to trim from the beginning of read 1. Default value: 0. This option can be set to 'null' to clear the default value.
Read1 max bases to write	The maximum number of bases to write from read 1 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
Read2 trim	The number of bases to trim from the beginning of read 2. Default value: 0. This option can be set to 'null' to clear the default value.
Read2 max bases to write	The maximum number of bases to write from read 2 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.

-sm2fq

SAM to FASTQ, more information please refer to Picard(http://picard.sourceforge.net/command-line-overview.shtml#SamToFastq).

The arguments is the same as -sm2fa.

-bm2sm

BAM to SAM.

-bm2fa

BAM to FASTA, the arguments is the same as -sm2fa.

-bm2fq

BAM to FASTQ, the arguments is the same as -sm2fq.

-psl2sm

PSL to SAM.

Arguments	Description
Match	The score that matches,default value: 1.
Mismatch	The score that mismatch, default value: 2.
Open	The score for gap open, default value: 5.
Extension	The score for gap extension, default value: 2.

-bw2sm

Bowtie to SAM.

-bd2bg

BED to BedGraph.

-wg2bd

Wig to BED.

-wg2bg

Wig to BedGraph.

Appendix B :Output naming rules

The output name follows the principles below:

Output file name is the same with input file and with the output format suffix.

If the above name is existed,then "_1" will add to the end of output name.The number will increase when there is still the same with anothor one.

So that,the output file will not overwrite any existed file.

These rules only effect on the build-in scripts.