Documentation requested for all output files

[lskatz]

Not all files are described when I used --keepfiles. Could there be documentation for them, even if it's not in the main documentation? The additional files are the files I had after a skesa run. I am adding onto your table.

Filename	Description
contigs.fa	The final assembly you should use
shovill.log	Full log file for bug reporting
shovill.corrections	List of post-assembly corrections
contigs.gfa	Assembly graph (spades)
contigs.fastg	Assembly graph (megahit)
contigs.LastGraph	Assembly graph (velvet)
skesa.fasta	Raw assembly (skesa)
spades.fasta	Raw assembled contigs (spades)
megahit.fasta	Raw assembly (megahit)
velvet.fasta	Raw assembly (velvet)
flash.extendedFrags.fastq.gz
flash.hist
flash.histogram
flash.notCombined_1.fastq.gz
flash.notCombined_2.fastq.gz
R1.cor.fq.gz	Corrected R1 reads from Ligher
R1.fq.gz	Original R1
R1.sub.fq.gz	Subsampled R1 using --depth
R2.cor.fq.gz	Corrected R2 reads from Ligher
R2.fq.gz	Original R2
R2.sub.fq.gz	Subsampled R2 using --depth
shovill.bam	Alignment of corrected reads from Trimmomatic against the vanilla assembly (skesa, spades, or megahit). Reads have been sorted with Samtools and filtered with samclip (ie, nuanced alignments have been removed).
shovill.bam.bai	Index file for shovill.bam
skesa.fasta.amb
skesa.fasta.ann
skesa.fasta.bwt
skesa.fasta.fai
skesa.fasta.pac
skesa.fasta.sa
skesa.fasta.uncorrected

[lskatz]

And my question leading into this was whether the bam file is all reads mapped against the assembly or only those trimmed/cleaned/flash'd.

[tseemann]

@lskatz can you look at the perl code and tell me? :)

The original (or trimmomaticked originals if --trim) are used for alignment/correction.

I do NOT use the FLASH ones because one of the potential errors I want to correct is mis-FLASH-ed reads.

[lskatz]

I took some language from

• https://wiki.gacrc.uga.edu/wiki/FLASH-Sapelo
• http://seqanswers.com/forums/showpost.php?p=90992&postcount=2

Filename	Description
contigs.fa	The final assembly you should use
shovill.log	Full log file for bug reporting
shovill.corrections	List of post-assembly corrections
contigs.gfa	Assembly graph (spades)
contigs.fastg	Assembly graph (megahit)
contigs.LastGraph	Assembly graph (velvet)
skesa.fasta	Raw assembly (skesa)
spades.fasta	Raw assembled contigs (spades)
megahit.fasta	Raw assembly (megahit)
velvet.fasta	Raw assembly (velvet)
flash.extendedFrags.fastq.gz	Single-end reads from Flash, ie, merged reads
flash.hist	Numeric histogram of merged read lengths.
flash.histogram	Visual histogram of merged read lengths.
flash.notCombined_1.fastq.gz	R1 reads not combined in Flash
flash.notCombined_2.fastq.gz	R2 reads not combined in Flash
R1.cor.fq.gz	Corrected R1 reads from Lighter
R1.fq.gz	Original R1
R1.sub.fq.gz	Subsampled R1 using --depth
R2.cor.fq.gz	Corrected R2 reads from Ligher
R2.fq.gz	Original R2
R2.sub.fq.gz	Subsampled R2 using --depth
shovill.bam	Alignment of corrected reads from Trimmomatic against the vanilla assembly (skesa, spades, or megahit). Reads have been sorted with Samtools and filtered with samclip (ie, nuanced alignments have been removed).
shovill.bam.bai	Index file for shovill.bam
skesa.fasta.amb	(bwa index) text file, to record appearance of N (or other non-ATGC) in the ref fasta.
skesa.fasta.ann	(bwa index) text file, to record ref sequences, name, length, etc.
skesa.fasta.bwt	(bwa index) binary, the Burrows-Wheeler transformed sequence.
skesa.fasta.fai	Samtools index file
skesa.fasta.pac	(bwa index) binary, packaged sequence (four base pairs encode one byte).
skesa.fasta.sa	(bwa index) binary, suffix array index.
skesa.fasta.uncorrected	Assembly before pilon correction