soapdenovo2

anneng

https://github.com/aquaskyline/SOAPdenovo2/issues/69
如上贴所述编译时报错

pregraph_sparse_63mer.v1.0.3 cleaning done.                         
pregraph_sparse_63mer.v1.0.3 objects generated.                    
SOAPdenovo-63mer cleaning done.                              
SOAPdenovo-63mer objects generated.                                
/usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam_import.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: ./sparsePregraph/inc/libbam.a(sam.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam_pileup.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: ./sparsePregraph/inc/libbam.a(faidx.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: ./sparsePregraph/inc/libbam.a(knetfile.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: ./sparsePregraph/inc/libbam.a(sam_header.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: ./sparsePregraph/inc/libbam.a(bgzf.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: ./sparsePregraph/inc/libbam.a(kstring.o): relocation R_X86_64_32 against `.text' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam_aux.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: ./sparsePregraph/inc/libbam.a(razf.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:56: recipe for target 'SOAPdenovo-63mer' failed
make: *** [SOAPdenovo-63mer] Error 1

下载老版本的samtools
https://sourceforge.net/projects/samtools/files/samtools/0.1.19/

替换 sparsePregraph/inc/libbam.a

很无奈！！！！

anneng

cd /home/bioinfo/soapdenovo2/SOAPdenovo2-r242
./SOAPdenovo-63mer all -s tobacco.config -K 63 -R -o tobacco

这个命令的输入文件是在配置文件里面写的建议用shell封装下把 R1 R2 暴露出来其他参数用配置文件也可以

anneng

Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis tomentella and Corydalis saxicola
https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.7312
2.2 Genome assembly and annotation
The cp genome were assembled on a Linux system. First, raw sequencing data were filtered using Trimmomatic (Version 0.36) to get the high-quality clean data (Bolger et al., 2014). In the second step, we used the thirteen chloroplast genome sequences of Papaveraceae species which were downloaded from GenBank to establish a Basic Local Alignment Search Tool (BLASTn) database. Then the clean data were mapped to the BLAST database, and the mapped reads which were considered as reads from chloroplast genome were extracted. Next step, the extracted reads were assembled to contigs using SOAPdenovo2 (Luo et al., 2012). At last, SSPACE was used to construct the scaffold of the chloroplast genome (Boetzer et al., 2011), and GapCloser was used to fill gaps (Luo et al., 2012). The completed genomes were annotated using CPGAVAS2 (Shi et al., 2019), and the results were modified for starter and terminator revisions by Apollo software (Lee et al., 2009). CPGAVAS2 software was used to convert revised GFF3 format annotation results into a sqn format for NCBI submission. Sequin software was used to check and correct unsatisfactory comments in the sqn file, and the corrected results were submitted to the NCBI database. Physical maps of the cp genomes were drawn by GenomeDRAW (Marc et al., 2013) using a GB format file exported from the sqn file by sequin software.

anneng

对组装的结果进行质控
docker pull staphb/quast

 quast.py test_data/contigs_1.fasta \
           test_data/contigs_2.fasta \
        -r test_data/reference.fasta.gz \
        -g test_data/genes.txt \
        -1 test_data/reads1.fastq.gz -2 test_data/reads2.fastq.gz \
        -o quast_test_output

anneng

a. *.contig
contig sequences without using mate pair information.
b. *.scafSeq
scaffold sequences (final contig sequences can be extracted by breaking down scaffold sequences at gap regions).