Scaffolding tool based on Hi-C reads.
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.
- zlib
Run the following commands to install pins:
git clone https://github.com/dfguan/pin_hic.git
cd pin_hic/src && make
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
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:
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.
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.
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
SAT format is extended from the GFA 1.0 format.
| Tag | Description | Comment |
|---|---|---|
| H | Header | optional |
| S | Sequence | required |
| L | Link | optional |
| P | Path | optional |
| A | Scaffold set | optional |
| C | Current scaffold set | optional |
| Col | Field | Regexp | Description | Comment |
|---|---|---|---|---|
| 1 | TAG | H |
Tag | Required |
| 2 | VER | VN:Z:[0-9]\.[0-9] |
Version | Required |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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
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].
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