I have a MeatG library, which was sequenced by two times. The first time, we got unpaired reads (i.e., unpaired.fastq); while we got interlaced forward and reverse paired-end reads (i.e., interlaced-paired.fastq) for the 2nd time. Since they are from the same library, I assembled them together and got the assembled scaffolds. Now I would like to align both of them (unpaired and interlaced paired reads) simultaneously to the assembled contigs using Bowtie2 version 2.3.4.1 to get one .sam file. Can Bowtie2 do this? Any suggestions are appreciated! 

I tried the following two scripts, the results for both were same. So for the first script, only the paired reads are mapped.

    bowtie2 -q --phred33 --end-to-end --sensitive -p 12 -I 0 -X 2000 --no-unal -x bowtie2-db/CBIW --interleaved interlaced-paired.fastq -U unpaired.fastq | samtools view -Sb - > output.bam
    
    bowtie2 -q --phred33 --end-to-end --sensitive -p 12 -I 0 -X 2000 --no-unal -x bowtie2-db/CBIW --interleaved interlaced-paired.fastq | samtools view -Sb - > output.bam



**See the align result:**

    Building a SMALL index
    
    35388893 reads; of these:
      
      35388893 (100.00%) were paired; of these:
      
    11580370 (32.72%) aligned concordantly 0 times
 
    23621928 (66.75%) aligned concordantly exactly 1 time
    
    186595 (0.53%) aligned concordantly >1 times
    
    11580370 pairs aligned concordantly 0 times; of these:
      
        101972 (0.88%) aligned discordantly 1 time
    
        11478398 pairs aligned 0 times concordantly or discordantly; of these:
      
            22956796 mates make up the pairs; of these:
        
                22513992 (98.07%) aligned 0 times
        
                432094 (1.88%) aligned exactly 1 time
        
                10710 (0.05%) aligned >1 times

    68.19% overall alignment rate
I don't think Bowtie2 can map paired- and single-end reads simultaneously, but you can merge both mappings with samtools. BWA can map map a mix of interleaved paired reads and single reads, if you concatenate both files and keep single reads at the end.

Use `samtools sort` to sort each bam by position, then `samtools merge` to merge the sorted bams into one.

If having a sorted bam is not important, you can just use `samtools cat`. 
