SEQ/PRB

The file names do not need to be identical, but they must be appended with the phrases “_seq” and “_prb” respectively. For example, SRR01842a_seq.txt and SRR01842c_prb.txt.

FASTQ (merged pairs)

Select this option for paired end files in FASTQ format that contain both reads in a pair in the same line in opposite orientation
(Read 1 -> <- Read2). NextGENe converts these files by splitting each read in two. Two new files are created titled *_1.fasta and *_2.fasta with read names >*/1 and >*/2. The second half of the original read and the quality scores are reverse complemented. The file is then converted to .fasta format and quality filtering is implemented as with other FASTQ files.

The SOLiD System instrument produces color space sequence reads in a .fasta format labeled as CSFASTA. If you select CFASTA as the input format type and FASTA as the output format type, then NextGENe converts the reads from color space to base space.

FASTA

Select this option and choose CSFASTA as the output format type to convert .fasta files in base space into .csfasta files in color space.

Mate Pair SFF

Select this option for mate-pair files in SFF format that contain both reads in a pair in the same line. NextGENe converts these files by splitting each read in two. Two new files are created titled *_1.fna and *_2.fna with read names >*/1 and >*/2. The file is then converted to .fasta format and quality filtering is implemented as with other SFF files.

Mate Pair FASTQ

Select this option for mate-pair files in FASTQ format that contain both reads in a pair in the same line. NextGENe converts these files by splitting each read in two. Two new files are created titled *_1.fna and *_2.fna with read names >*/1 and >*/2. The file is then converted to .fasta format and quality filtering is implemented as with other FASTQ files.

Median score threshold >= [20]

Selected by default. Removes entire reads from the sample file when the median quality score is below the specified threshold.

Max # of uncalled bases <= [3]

Selected by default. Remove entire reads from the sample file when the contains more N calls then specified.

Called base number of each read >= [25]

Selected by default. Trims low quality bases from reads when a consecutive number of bases (“x”) falls below the specified qualify score threshold (“y”).

Trim or reject read when >= [3] base(s) with score <= [16]

Selected by default. Trims low quality based from reds when a consecutive number of bases (“x”) falls below the specified quality score threshold (“y”).

Paired read data

Available only if paired read data is being analyzed. Select this option if you are converting a mate-paired or paired-end files. NextGENe uses a placeholder “N” for reads that are removed because of low quality, which is necessary to maintain mate-paired or paired-end read information.

Remove 5’ [2] bases and 3’ [4] bases

Trims the specified number of bases from the 5’ and/0r 3’ ends.

Keep only bases [0] to [0]

Trims the reads to keep the only the specified portion of the read.

Trim by sequences

Select this option to trim reads where the specified sequence occurs. See Trim by Sequences.

Trim by sequences in file

Select this option and then click the Browse button load a tab-delimited text file that contains the sequences by which the reads are to be trimmed. See Trim by Sequences in the File.

Custom linker

Applicable only for mate-paired Roche data or mate-paired Ion Torrent data where both pairs are located in the same read. Select this option if you used a custom linker. NextGENe automatically detects the standard linker sequences.