mapping-illumina~bwa_mem

input_1:paired-end FASTQ(.gz) files

input_1/SRR4425244_1.fastq

@SRR4425244.1 1 length=101
CTGTNCTACTCCATCGTTGAAAATCTCGCCATTGGGAACTTGAGGCGCAGGAAGGGGCAGCTCCTCAACTGGCAACACTGGTTCCGGTACAACCGGATCTA
+SRR4425244.1 1 length=101
@@@D#2ADFHHHDGII@GHIIIFGIIIIGIIEGEBFHIIIIEGIIIIHIIGEHFDBECCC@CCCACCCCCACBCABBBCCBCCCC995>BCC:<@B<BBCC
@SRR4425244.2 2 length=101
CCCGCATTCCATTGCCAATGGTTTCAAGAACCTTTTGGCCATCGCTGCTGTCACAGAGGTTGAGTTTGAAGAAGCTACCACCATCAAGGAGTTCATTAAGN
+SRR4425244.2 2 length=101
?@@DBDDFDFADHGGIIICCG:BFHIIGE;EFBGHIGGGGIGGGIHIIIH=BGBDGEHG=@GGG=EHH;;3?C);;?>>@C?B@CCCCCBBCAAC>C@AC=
@SRR4425244.3 3 length=101
AAACTCCAGGCTTAAAAGCAATTTTTATAAAAAAAAATACAAGTAGAATAAAAAAAGAGCTTTGTTGCCCGTTTTTTCAAAAGTAACAAATTGTATCATAT

input_1/SRR4425244_2.fastq

@SRR4425244.1 1 length=101
CCTGAACCTGTTTTCCCGGTGGAACCATCTGAACCTGTCGTCCCCGTAGAACCATCTGAACCTGTTATCCCCGTGGAACCTGAGCCCATCGATAATCCTTC
+SRR4425244.1 1 length=101
@C@FFDFFHHDFDGIIIIA@FHGGGJIJHGIIJBHEHFHCDGHDGF<8FHFHGICHFHHEHFBD?CCCCEEC83;@@CCB<9?<CAB?CC@9?BBCACC4:
@SRR4425244.2 2 length=101
CGCTTTCTTCCTCCTCTTTTTCTTCTTTCTTTTCCTCCTTCTTCTCAGCCGGAGCAGCGGCGGCGGACGGTGCCACCGCGGCAGCAACTGCAGCGAACTTT
+SRR4425244.2 2 length=101
B@@FFFADHHFHGGIEI>AHF?FH@HHIJFDHIHEH?BGHBFD<BBI@BF@HG<FH>D</:9?=>B-80;&2-9>:<><95-&0<?A839@##########
@SRR4425244.3 3 length=101
GAATGATTAAAATACAATAAATTGAAGACGTGAGTGGATGAAGGGATATGATACAATTTGTTACTTTTGAAAAAACGGGCAACAAAGCTCTTTTTTTATTC

input_1/SRR4425245_1.fastq

@SRR4425245.1 1 length=100
AATTTAGAATCAACATGATTTGCAGAGTTTAAAGAATCAAAACGAATCGAGTAATTTTACTCATTTGAGATCCGTGCTTCTAGCACAACCAGTCTTCCAN
+SRR4425245.1 1 length=100
@<?;?BBDBF<DFFHHII<FHD9CF@FH@HGGCH@>BAGCGD@F??:8?BFDFGIGGGGGGIGG;FHC=DCG>G?;8?;?;CBCC>ACBBBB5A@CAAA:
@SRR4425245.2 2 length=100
NCCTAGTCCAGCGTCATCGTCTCCATTTCCATGCCCATGTCCATGAACTCCAATACCAGCACCAACTCCTAGTCCAGCGTCATCGTCTCCATTTCCATGC
+SRR4425245.2 2 length=100
#1=DFFFFHHGHHJJIJJJGIHIIIJJIGEGIGIIIEE;DGIIJIJIJIIJJIHIGHIHIHIJIIJGHIFEH=CEB?DCABDDDDDDDDDDDEEEDDDCC
@SRR4425245.3 3 length=100
TTTACATACAATAAATTTTATCAAGCAATTTTTAAGTCTTAGTATTTTCTCAATTATCAATTTGAAAAATTTGTTAATTGTCTCTATATAGTAAAATCCA

input_1/SRR4425245_2.fastq

@SRR4425245.1 1 length=100
CTCGGTTCGGTTAGGAAATATCAGGGTCTGGAAGACTGGTTGTGCTAGAAGCACGGATCTCAAATGAGTAAAATTACTCGATTCGTTTTGATTCTTTAAA
+SRR4425245.1 1 length=100
?BBF?+@DFFA8CFBEFEGGHGIIEIGAFGEIGIBB@<DFFG?DGG@48CDGGDH8;A4?;=>D;BBB>A>;>;>C@;@==CCC@CCDDD?CDDDDD###
@SRR4425245.2 2 length=100
CTAGGACTAGGTATTGGTGCCGGAATTCATGGACATGAACATGGAAATGGAGACGGTAACGCTGAGCTAGGAGTTGGTGCTGGTGTTGGAGTTCATGGAC
+SRR4425245.2 2 length=100
@CCFFDFFDHHAFGGIJIJJIJJJIJJJJIIIEGIIIJIJJIIJJIIHJJJGHGIIHCEDEEHFDFFFDEE>A@CCD;?CDDD,<<?BA@C@CD@CDDCD
@SRR4425245.3 3 length=100
CGAAAAAGAAAACTTTTTGAAATTGGCAGTGAGAGTGAAATACAGTGGATTTTACTATATAGAGACAATTAACAAATTTTTCAAATTGATAATTGAGAAA

input_2:reference genome file

input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa

>Bomo_Chr1
CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC
CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC
CTAACCTAATAACCTAACCTAACCTAACCTAACCTTAACCTAACCTAACCTAACCTAACCTAACCTAACC
TAACCTAACCTAACCTAACCTAACCTACCTTAACCTAACTAACCTAACCTAACCTAACCTAACCTAACCT
AACCTAACCTAAACCAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT
AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT
AACCTTAACCTAACCTAACCTAACCTAACCTAACCAACCTAACCTAACCTAACCTAACCTAACCTAACCT
AACCTAACCTAACCTAACCTAACCTAAAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC
CTAACCTAACCTAACCTAACCTAACTAACCTAACCTACCTAACCTAACCTAAACCTAACCTAACCTAACC

input_3:bwa index

input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.amb

460282090 695 30
18622205 100 N
65038045 100 N
66826208 26161 N
79159810 100 N
89456377 26446 N
101957359 53974 N
114592323 12481 N
139912238 43453 N
158639567 100 N

input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.ann

460282090 695 11
0 Bomo_Chr1 (null)
0 20666287 1
0 Bomo_Chr2 (null)
20666287 8396445 0
0 Bomo_Chr3 (null)
29062732 15212953 0
0 Bomo_Chr4 (null)
44275685 18737234 0
0 Bomo_Chr5 (null)

input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.bwt

input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.pac

input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.sa

Option

Output

output.bwa/SRR4425244.bam

output.bwa/SRR4425245.bam