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Pin_hic (Hi-C拼接)

Scaffolding tool based on Hi-C reads.

Overview

Pin_hic is a scaffolder using Hi-C data. It applies a dual selection and local optimal strategy to bridge two contigs and output a SAT file for each iteration, the SAT format is the extension of GFA format which is able to record the scaffolding process, and can also be useful for further genomic analysis.

Dependencies

  1. zlib

Installation

Run the following commands to install pins:

git clone https://github.com/dfguan/pin_hic.git
cd pin_hic/src && make

Usage

Scaffolding with Hi-C reads

Hi-C Read preprocessing

Given a list hiclist of Hi-C read files (suppose in fastq.gz format, paired files in a line) and the assembly asm, use the following code to generate Hi-C alignment files.

bwa index $asm
while read -r r1 r2
do
	prefix=`basename $r1 .fastq.gz`
	bwa mem -SP -B10 -t12 $asm $prefix_1.fq.gz $prefix_2.fq.gz | samtools view -b - > $prefix.bam
done < $hiclist
Hi-C scaffolding

Given Hi-C reads alignment bams, a draft assembly asm and a output directory outdir, if you want to build scaffols with Hi-C in N (default: 3) rounds, please try the following commands. The final assembly will be named as scaffols_final.fa.

samtools faidx $asm 
./bin/pin_hic_it -i $N -x $asm.fai -r $asm -O $outdir $bam1 $bam2 $bam3 ... 

Or you want to build scaffolds step by step:

Step 1. contact matrix calculation

From a draft assembly asm

samtools faidx $asm
./bin/pin_hic link $bam1 $bam2 $bam3 ... > link.matrix  # this will calcuate contact numbers between any pairs of contigs.

From a sat file:

./bin/pin_hic link -s $sat $bam1 $bam2 $bam3 ... > link.matrix  # this will calcuate contact numbers between any pairs of contigs.
Step 2. Scaffolding graph construction

From a draft assembly asm:

/bin/pin_hic build -w100 -k3 -c $asm.fai link.matrix > scaffolds.sat # this will generate scaffolding paths. 

From a sat file:

/bin/pin_hic build -w100 -k3 -s $sat link.matrix > scaffolds.sat # this will generate scaffolding paths. 
Step 3. Mis-join detection

Given a sat file:

./bin/pin_hic break $sat $bam1 $bam2 $bam3 ... > scaffs.bk.sat
./bin/pin_hic gets -c $asm scaffs.bk.sat > scaffols_final.fa # get scaffold sequences.

A scaffolding pipeline of 3 iterations:

samtools faidx $asm
for i in `seq 1 3`
do
	if [ $i -eq 1 ]
	then 
		./bin/pin_hic link $bam1 $bam2 $bam3 ... > links_$i.matrix
		./bin/pin_hic build -w100 -k3 -c $asm.fai links_$i.matrix > scaffolds_$i.sat
	else
		./bin/pin_hic link -s scaffolds_$pi.sat $bam1 $bam2 $bam3 ... > links_$i.matrix
		./bin/pin_hic build -w100 -k3 -s scaffolds_$pi.sat links_$i.matrix > scaffolds_$i.sat 
	fi
	pi=i
done
./bin/pin_hic break -s scaffolds_$i.sat $bam1 $bam2 $bam3 ... > scaffolds_bk.sat 
./bin/pin_hic gets -c $asm scaffs.bk.sat > scaffols_final.fa 

Output format: SAT (V 0.1)

SAT format is extended from the GFA 1.0 format.

Record types

Tag Description Comment
H Header optional
S Sequence required
L Link optional
P Path optional
A Scaffold set optional
C Current scaffold set optional

H Header

Col Field Regexp Description Comment
1 TAG H Tag Required
2 VER VN:Z:[0-9]\.[0-9] Version Required

S Sequence

Col Field Regexp Description Comment
1 TAG S Tag Required
2 SNAME .+ Sequence name Required, primary key
3 SLEN [0-9]+ Sequence length Required
4 SEQ \*|[A-Za-z]+ Sequence Required

L Link

Col Field Regexp Description Comment
1 TAG P Tag Required
2 SRCS .+ Source sequence name Required, foregin key S:SNAME
3 SRCE [-+] Source end Required, + for 5' end and - for 3'
4 TGTS .+ Target sequence name Required, foregin key S:SNAME
5 TGTE [-+] Target end Required, + for 5' end and - for 3'
6 WGT wt:f:[0-9]*\.?[0-9]+ Link weight Optional

P Path

Col Field Regexp Description Comment
1 TAG P Tag Required
2 PNAME [cu][0-9]{9} Path name Required, primary key
3 PLEN [0-9]+ Path length Required
4 NAMEL ((.+[-+],)*(.+[-+]))|((u[0-9]{9}[-+],)*u[0-9]{9}[-+]) List of sequence names or path names Required, foregin keys S:SNAME

A Scaffold set (or assembly set ?)

Col Field Regexp Description Comment
1 TAG A Tag Required
2 ANAME a[0-9]{5} Scaffold set name Required
3 PNAMEL ([cu][0-9]{9},)*[cu][0-9]{9} List of path names Required, foregin keys P:PNAME
C Current scaffold set
Col Field Regexp Description Comment
1 TAG C Tag Required
2 CNAME a[0-9]{5} Current scaffold set name Required, foregin key A:ANAME

Example

H	VN:Z:0.1
S	LR132056.1.4	138023	*
S	LR132056.1.5	1128790	*
S	LR132056.1.6	4496575	*
P	u000000004	662215	LR132053.1.4+,LR132053.1.5+,LR132053.1.6+
L	LR132051.1.5	+	LR132051.1.4	-	wt:f:0.028248
L	LR132051.1.6	+	LR132051.1.5	-	wt:f:0.009367
A	a00000	1	u000000004
C	a00000

Limitation

FAQ

Contact

Every one is Wellcomed to use and distribute the package. Bug report or any other suggestions, please use the github webpage or email me [email protected].

pin_hic's People

Contributors

dfguan avatar

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