A gap-closing software tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly.
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Both raw reads and pre-error-corrected reads are acceptable as input.
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If only raw long reads are provided, it polishes raw TGS reads by calling Racon.
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If additional NGS short reads are available, it polishes raw TGS reads by calling Pilon.
Notice : only fasta format of TGS reads is acceptable.
If you use TGS-GapCloser in your work, please cite: TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads Mengyang Xu, Lidong Guo, Shengqiang Gu, Ou Wang, Rui Zhang, Brock A Peters, Guangyi Fan, Xin Liu, Xun Xu, Li Deng, Yongwei Zhang GigaScience, Volume 9, Issue 9, 1 September 2020, giaa094, https://doi.org/10.1093/gigascience/giaa094
- gcc 4.4+
- make 3.8+
git clone https://github.com/BGI-Qingdao/TGS-GapCloser.git YOUR-INSTALL-DIR
- If you have already installed a minimap2, then link it here
rm -rf YOUR-INSTALL-DIR/minimap2
ln -s MINIMAP2-PATH YOUR-INSTALL-DIR/
- Otherwise you need to download it by:
cd YOUR-INSTALL-DIR
git submodule init
git submodule update
cd YOUR-INSTALL-DIR
make
conda install -c bioconda tgsgapcloser
if your install by conda, please install minimap2 first and make sure that minimap2 is available in your environment.
Usage:
tgsgapcloser --scaff SCAFF_FILE --reads TGS_READS_FILE --output OUT_PREFIX [options...]
required:
--scaff <draft scaffolds> input draft scaffolds.
--reads <TGS reads> input TGS reads.
--output <output prefix> output prefix.
## error correction module
--ne do not execute error correction.
or
--racon <racon> installed racon. Can be installed following https://github.com/isovic/racon
or
--pilon <pilon> pilon jar package. Can be downloaded from https://github.com/broadinstitute/pilon/releases/download/v1.23/pilon-1.23.jar
--java <java> installed java.
--ngs <ngs_reads> input NGS reads used for pilon.
--samtools <samtools> installed samtools.
optional:
--minmap_arg <minmap2 args> like --minmap_arg \' -x ava-ont\'
the arg must be wraped by \' \'
--tgstype <pb/ont> TGS type. ont by default.
--min_idy <float> minimum identity for filtering candidate sequences.
0.3 for ont by default.
0.2 for pb by default.
--min_match <int> minimum matched length for filtering candidate sequences.
300 for ont by default.
200 for pb by default.
--thread <int> number of threads uesd. 16 by default.
--pilon_mem <int> memory used for pilon, passing to -Xmx. can use “m” or “M” for MB, or “g” or “G” for GB. 300G by default.
--chunk <int> split candidates into # of chunks to separately correct errors. 3 by default.
--p_round <int> iteration number for pilon error-correction. 3 by default.
--r_round <int> iteration number for racon error-correction. 1 by default.
--g_check gapsize diff check , none by default.
--min_nread <int> minimum number of reads that can bridge this gap. 1 by default.
--max_nread <int> maximum number of reads that can bridge this gap. -1 by default.
--max_candidate <int> maximum number of candidate alignment used for error correction and gapfilling. 10 by default
WARNING : only fasta format TGS reads is supperted and fastq format will lead to program carshing !
YOUR-INSTALL-DIR/tgsgapcloser \
--scaff scaffold-path/scaffold.fasta \
--reads tgs-reads-path/tgs.reads.fasta \
--output test_ne \
--ne \
>pipe.log 2>pipe.err
YOUR-INSTALL-DIR/tgsgapcloser \
--scaff scaffold-path/scaffold.fasta \
--reads tgs-reads-path/tgs.reads.fasta \
--output test_racon \
--racon racon-path/bin/racon \
>pipe.log 2>pipe.err
YOUR-INSTALL-DIR/tgsgapcloser \
--scaff scaffold-path/scaffold.fasta \
--reads tgs-reads-path/tgs.reads.fasta \
--output test_pilon \
--pilon pilon-path/pilon-1.23.jar \
--ngs ngs-reads-path/ngs.reads.fastq.gz \
--samtools samtools-path/bin/samtools \
--java java-path/bin/java \
>pipe.log 2>pipe.err
- default TGS type is ONT, use
--tgstypeto change it .
--tgstype ont
to
--tgstype pb
- an example of raw Pacbio reads with error correction using long reads only
YOUR-INSTALL-DIR/tgsgapcloser \
--scaff scaffold-path/scaffold.fasta \
--reads tgs-reads-path/tgs.reads.fasta \
--output test_racon \
--racon raconn-path/bin/racon \
--tgstype pb \
>pipe.log 2>pipe.err
Use --minmap_arg ' your-own minimap2 args'
This is useful when your want to avoid a huge paf file.
for example , if your use HiFi Reads , you may try --minmap_arg '-x asm20'
YOUR-INSTALL-DIR/tgsgapcloser \
--scaff scaffold-path/scaffold.fasta \
--reads tgs-reads-path/tgs.reads.fasta \
--output test_racon \
--minmap_arg '-x asm20' \
--racon raconn-path/bin/racon \
--tgstype pb \
>pipe.log 2>pipe.err
- your-prefix.scaff_seq
- this is the final assembly after gap filling
- your-prefix.gap_fill_details
- details about how the final assembly was assemblied
>scaffold_1
1 1000 S 1000 2000
1001 1010 N
1011 1100 S 2201 2290
1101 1110 F
1111 1200 S 2301 2390
>scaffold_2
......
- each scaffold name is followed by its data lines.
- a data line consists of 3 or 5 columns and describes the source of each segment in the final sequence:
- column 1 is the segment's first bp position in the final sequence.
- column 2 is the segment's last bp position in the final sequence.
- column 3 is the segment's type , 'S' , 'N' or 'F'.
- 'S' means this segment is a segment of the input sequence and this line includes other two more columns:
- column 4 is the segment's first bp position in the input sequence.
- column 5 is the segment's last bp position in the input sequence.
- 'N' means this segment is a N area.
- 'F' means this segment is a filled sequence from TGS reads.
- 'S' means this segment is a segment of the input sequence and this line includes other two more columns:
Any questions, please feel free to ask xumengyang@genomics.cn or guolidong@genomics.cn