FxTools

FxTools: a comprehensive toolkit for FASTA and FASTQ file manipulation

FxTools is a full-featured toolkit for comprehensive analysis of both FASTA and FASTQ file, covering users' needs from sequence modification to data analysis. This tool consists of three parts: Fatools , Fqtools and Formtools, categorized by the types of files to deal with. In Formtools, we provide simple conversion and file manipulation for other NGS data files including BAM,SAM and SOAP. FxTools is implemented in C/C++ language, available for Linux and Mac OS X operating system.

1) Download and Install

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The new version will be updated and maintained in hewm2008/FxTools, please click below website to download the latest version

hewm2008/FxTools

Download
 
Pre-installations of 4 libraries are required before installing FxTools  
1 htslib: samtools-1.6/htslib-1.6  
2 boost : boost with g++ > 4.9 is recommended  
3 zlib : zlib > 1.2.8 is recommended
4 ncurses: ncurses >5.7 is recommended

For linux /Unix statics

• you can use the statically compiled programs directly

       git clone https://github.com/hewm2008/FxTools.git
       cd FxTools-XXX;  
       chmod 775 bin/FxTools_Linux ; 
       ./bin/FxTools_Linux

• To compile FxTools, do [./configure] first and than [make]
• Final software can be found in the direcoty [bin/FxTools]

For linux/Unix or MacOS

        git clone https://github.com/hewm2008/FxTools.git
        cd FxTools-XXX;
        chmod 755 configure ; ./configure
        make ;
        mv FxTools bin/;
	./bin/FxTools

Note1: If fail in [./configure], to find library htslib, you can add LDFLAGS to find the htslib library and CXXFLAGS and CFLAGS to find the htslib header [ ./configure LDFLAGS=-L/usr/lib/ CXXFLAGS=-I/usr/include/ CFLAGS=-I/usr/include/];
export 'LIBRARY/CFLAGS/CXXFLAGS' environment variables to set the htslib path also can be a way to compile, such : export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH;

2) Features

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Parameter description

Program: FxTools
Version: 0.16   [email protected]/[email protected]     2018-5-20

        Usage:

                Fatools        Tools For Fasta
                Fqtools        Tools For Fastq
                Formtools      Tools For Form convert

                Help           Show help in detail

Fatools

Module	Function	Description
Summary
	stat	statistics of FASTA
	dict	generate a header file for FASTA
Split
	split	split FASTA. default by ID
	rand	randomly sample FASTA by proportion
Search
	findN	find the regions of N in FASTA file
	locate	find the region containing the subsequences
	grep	search for the target subsequence
	extractP	extract sequences with specific ID
	extractN	extract sequences by specified order range
	getCdsPep	find CDS & peptide sequences (GFF re-quired)
	sort	sort the FASTA by sequence ID or length
Modify
	filter	remove the sequences either too short or with too many missing N
	reform	edit the FASTA (reverse, complement,etc.)
	mergaSca	reform current FASTA into new scaffolds
	JoinSca	joining scaffolds into pseudo chromosomes
	BaseModify	modify a single base in FASTA
	ChangePosi	locate SNPs on original scaffolds based on current FASTA

Fqtools

Module	Function	Description
Summary
	valid	check validation of input FASTQ
	stat	statistics of FASTQ
	fqcheck	base and quality distribution
Split
	splitpool	split pooling FASTQ to samples for RAD (GBS)
	splitFq	split FASTQ by specifying number of sequences in output
	cut	extract subsequence in FASTQ
	rand	randomly sample FASTQ by proportion
Modify
	filter	filter FASTQ to clean dataset
	rmAdapter	remove adapter of FASTQ
	reform	edit the FASTQ file (reverse/complement)
	Mul2Sin	covert multiple-lines FASTQ sequences to single line
	bubble	filter regions with large number of N
	changeQ	update the quality of FASTQ
	rmDup	remove duplicated sequences

Formtools

Function	Description
CDS2Pep	convert CDS to Pep format
Soap2fq	convert SOAP to FASTQ format
Bam2Fq	convert BAM to FASTQ format
Soap2Bam	convert SOAP to Bam/Sam format
Bam2SOAP	convert BAM/SAM to SOAP format
Fa2Fq	convert FASTA to FASTQ format
Fq2Fa	convert FASTQ to FASTA format
SF	finding intersections or differences of two files
Merge	merge sorted files to one

3) Examples

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see more other Usage in the Manual Documentation

• 1. sort fa files

   # sort by seq length
   ./bin/FxTools  Fatools sort    -i  ref.fa      -s   length   -r    > ref.sort.fa
   #  sort by seq ID & gzip out 
   ./bin/FxTools  Fatools sort    -i  ref.fa      -s  name  -o  ref.sort.fa.gz

• 2. split the fa files

# split by one seq on file 
	./FxTools  Fatools split   -i   in.fa.gz    -o outDir/ -g
# split to fixed Number of subflie 
	./FxTools  Fatools split   -i   in.fa       -o outDir/  -f 12 
# split to fixed seq Number in one sub-file 
        ./FxTools  Fatools split   -i   in.fa       -o outDir/  -s 12 

• 3. Calculate qulity of fq files

# Give pdf of fastq  Base Q Distribute and stat result
	 ./FxTools  Fqtools   fqcheck  -i A_1.fq.gz    A_2.fq.gz  -o out1Prefix  out2Prefix 
# SE fqstq also can be supported 
	 ./FxTools  Fqtools   fqcheck  -i A.fq.gz   -o outPrefix 

• 4. change qulity of fq

#  fstaq Q change : by ASCII33-->ASCII64[+31] with ResetID & MaxQ:h
	./FxTools  Fqtools   changeQ   -i in.fq.gz   -o out.fq  -s 4 

see more other Usage in the Documentation

4) Format

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Format Introduction

• FASTA format
• FASTQ format
• sam/bam format
• soap format
  chinese soap introduction

5) discussion

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• 📧 [email protected] / [email protected] / [email protected]
• join the QQ Group : 125293663

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