https://sourceforge.net/p/overlapper-reads/wiki/Home/Recent changes to HomeenMon, 13 Aug 2018 14:26:48 -0000https://sourceforge.net/p/overlapper-reads/wiki/Home/<div class="markdown_content"><pre>--- v15 +++ v16 @@ -8,6 +8,11 @@ ### Requirements ### * Python 3+ + +### How to Cite### +If you use OverlapPER, please cite: + +Oliveira, R. R. M., Nunes, G. L., de Lima, T. G. L., Oliveira, G., &amp; Alves, R. (2018). PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly. BMC Bioinformatics, 19(1). doi:10.1186/s12859-018-2307-y ### Usage ### </pre> </div>Renato OliveiraMon, 13 Aug 2018 14:26:48 -0000https://sourceforge.net71d598b1783bc0d18ea9484d4f8663ff686b6e4bhttps://sourceforge.net/p/overlapper-reads/wiki/Home/<div class="markdown_content"><pre>--- v14 +++ v15 @@ -2,7 +2,7 @@ OverlapPER may be used to merge overlapping paired-end reads - + **Figure 1 - Merging process for paired-end reads. (A) OverlapPER script first finds a seed (a short sequence in one of the reads represented in bold) (B) The reads are positioned according to the seed found and the total overlap is determined. (C). The total overlap is analyzed. If there is a hit in the alignment, the identity score is incremented. If a base is aligned to a gap, the identity score is incremented. In case of a mismatch in the alignment, if the next 5 bases (tolerance) are identical, the mismatch score is incremented, otherwise a gap insertion is repeated 4 times until the next 5 bases are identical. Nucleotides in bold represent a hit in the alignment.** ### Requirements ### </pre> </div>Renato OliveiraWed, 13 Jun 2018 20:36:50 -0000https://sourceforge.net91801773464e92efbd61980674948a845c7e9f4bhttps://sourceforge.net/p/overlapper-reads/wiki/Home/<div class="markdown_content"><pre>--- v13 +++ v14 @@ -46,7 +46,7 @@ ### OverlapPER performance ### **Table 1 - Results obtained by OverlapPER, PEAR, FLASH and COPE. ** - + Parameters: minimum overlap of 10 bp and minimum identity of 90%. Mean identity, mismatch and gap openings are shown in comparison to the reference genome. The wiki uses [Markdown](/p/overlapper-reads/wiki/markdown_syntax/) syntax. </pre> </div>Renato OliveiraThu, 17 May 2018 16:21:11 -0000https://sourceforge.neta1cbd3a1d5cf31a2f9f5dfcbc90d129efb1d685bhttps://sourceforge.net/p/overlapper-reads/wiki/Home/<div class="markdown_content"><pre>--- v12 +++ v13 @@ -46,7 +46,7 @@ ### OverlapPER performance ### **Table 1 - Results obtained by OverlapPER, PEAR, FLASH and COPE. ** - + Parameters: minimum overlap of 10 bp and minimum identity of 90%. Mean identity, mismatch and gap openings are shown in comparison to the reference genome. The wiki uses [Markdown](/p/overlapper-reads/wiki/markdown_syntax/) syntax. </pre> </div>Renato OliveiraThu, 17 May 2018 16:18:03 -0000https://sourceforge.netbbea2e36933a190e86f56c802e891f20f2b258b3https://sourceforge.net/p/overlapper-reads/wiki/Home/<div class="markdown_content"><pre>--- v11 +++ v12 @@ -2,17 +2,33 @@ OverlapPER may be used to merge overlapping paired-end reads - -**Figure S1 - OverlapPER merging process for paired-end reads. (A) OverlapPER first finds a seed (a short sequence in one of the reads) (B) The reads are positioned according to the seed found and the total overlap is determined. (C) The ideal alignment is found in order to obtain an accurate consensus. Nucleotides in bold represent a hit in the alignment.** + +**Figure 1 - Merging process for paired-end reads. (A) OverlapPER script first finds a seed (a short sequence in one of the reads represented in bold) (B) The reads are positioned according to the seed found and the total overlap is determined. (C). The total overlap is analyzed. If there is a hit in the alignment, the identity score is incremented. If a base is aligned to a gap, the identity score is incremented. In case of a mismatch in the alignment, if the next 5 bases (tolerance) are identical, the mismatch score is incremented, otherwise a gap insertion is repeated 4 times until the next 5 bases are identical. Nucleotides in bold represent a hit in the alignment.** ### Requirements ### -* Python 2.7+ +* Python 3+ ### Usage ### -python overlapper.py &lt;forward_reads.fastq&gt; &lt;reverse_reads.fastq&gt; &lt;min_overlap_length&gt; &lt;min_overlap_similarity&gt; &lt;reads_separator&gt; -Ex: python overlapper.py forward_reads.fastq reverse_reads.fastq 15 0.9 _ +python overlapper.py -f &lt;forward_reads.fastq&gt; -r &lt;reverse_reads.fastq&gt; --mo &lt;min_overlap&gt; --ms &lt;min_similarity&gt; +Ex: python overlapper.py -f forward_reads.fastq -r reverse_reads.fastq --mo 15 --ms 0.9 + +OverlapPER: Overlapping Paired-End Reads +Usage: python overlapper.py [options] +Options: + -h + Show this message. + -f + Path to forward reads + -r + Path to reverse reads + --mo + Length of the minimum overlap between the paired + reads (Default 25). + --ms + Percentage of the accepted minimum similarity in an overlap + region oftwo paired reads (default is 0.9). ### Contributors ### </pre> </div>Renato OliveiraThu, 17 May 2018 16:13:28 -0000https://sourceforge.net8a41c5659305671f0c9aa8dc4d4de74327a8647chttps://sourceforge.net/p/overlapper-reads/wiki/Home/<div class="markdown_content"><pre>--- v9 +++ v10 @@ -2,7 +2,7 @@ OverlapPER may be used to merge overlapping paired-end reads - + **Figure S1 - OverlapPER merging process for paired-end reads. (A) OverlapPER first finds a seed (a short sequence in one of the reads) (B) The reads are positioned according to the seed found and the total overlap is determined. (C) The ideal alignment is found in order to obtain an accurate consensus. Nucleotides in bold represent a hit in the alignment.** ### Requirements ### @@ -30,7 +30,7 @@ ### OverlapPER performance ### **Table 1 - Results obtained by OverlapPER, PEAR, FLASH and COPE. ** - + Parameters: minimum overlap of 10 bp and minimum identity of 90%. Mean identity, mismatch and gap openings are shown in comparison to the reference genome. The wiki uses [Markdown](/p/overlapper-reads/wiki/markdown_syntax/) syntax. </pre> </div>Renato OliveiraFri, 12 Aug 2016 19:24:11 -0000https://sourceforge.netf76d184a87585f2e6031c4a181031aa17d66c300https://sourceforge.net/p/overlapper-reads/wiki/Home/<div class="markdown_content"><pre>--- v8 +++ v9 @@ -3,7 +3,7 @@ OverlapPER may be used to merge overlapping paired-end reads  -Figure S1 - OverlapPER merging process for paired-end reads. (A) OverlapPER first finds a seed (a short sequence in one of the reads) (B) The reads are positioned according to the seed found and the total overlap is determined. (C) The ideal alignment is found in order to obtain an accurate consensus. Nucleotides in bold represent a hit in the alignment. +**Figure S1 - OverlapPER merging process for paired-end reads. (A) OverlapPER first finds a seed (a short sequence in one of the reads) (B) The reads are positioned according to the seed found and the total overlap is determined. (C) The ideal alignment is found in order to obtain an accurate consensus. Nucleotides in bold represent a hit in the alignment.** ### Requirements ### @@ -29,8 +29,8 @@ ### How to cite ### ### OverlapPER performance ### -Table 1 - Results obtained by OverlapPER, PEAR, FLASH and COPE. - +**Table 1 - Results obtained by OverlapPER, PEAR, FLASH and COPE. ** + Parameters: minimum overlap of 10 bp and minimum identity of 90%. Mean identity, mismatch and gap openings are shown in comparison to the reference genome. The wiki uses [Markdown](/p/overlapper-reads/wiki/markdown_syntax/) syntax. </pre> </div>Renato OliveiraWed, 10 Aug 2016 15:39:53 -0000https://sourceforge.net408ba6236d0163a556d2ff64c7718036bf42357dhttps://sourceforge.net/p/overlapper-reads/wiki/Home/<div class="markdown_content"><pre>--- v7 +++ v8 @@ -2,7 +2,7 @@ OverlapPER may be used to merge overlapping paired-end reads - + Figure S1 - OverlapPER merging process for paired-end reads. (A) OverlapPER first finds a seed (a short sequence in one of the reads) (B) The reads are positioned according to the seed found and the total overlap is determined. (C) The ideal alignment is found in order to obtain an accurate consensus. Nucleotides in bold represent a hit in the alignment. ### Requirements ### </pre> </div>Renato OliveiraWed, 10 Aug 2016 15:37:32 -0000https://sourceforge.net16e9fb0db71e2fa3c7c50b33f5ff9dd919cb30b2https://sourceforge.net/p/overlapper-reads/wiki/Home/<div class="markdown_content"><pre>--- v6 +++ v7 @@ -2,7 +2,7 @@ OverlapPER may be used to merge overlapping paired-end reads - + Figure S1 - OverlapPER merging process for paired-end reads. (A) OverlapPER first finds a seed (a short sequence in one of the reads) (B) The reads are positioned according to the seed found and the total overlap is determined. (C) The ideal alignment is found in order to obtain an accurate consensus. Nucleotides in bold represent a hit in the alignment. ### Requirements ### </pre> </div>Renato OliveiraWed, 10 Aug 2016 15:27:28 -0000https://sourceforge.net6b58ac2106d96d3ed23e35a38f24d6d05339057ahttps://sourceforge.net/p/overlapper-reads/wiki/Home/<div class="markdown_content"><pre>--- v5 +++ v6 @@ -2,7 +2,7 @@ OverlapPER may be used to merge overlapping paired-end reads - + Figure S1 - OverlapPER merging process for paired-end reads. (A) OverlapPER first finds a seed (a short sequence in one of the reads) (B) The reads are positioned according to the seed found and the total overlap is determined. (C) The ideal alignment is found in order to obtain an accurate consensus. Nucleotides in bold represent a hit in the alignment. ### Requirements ### </pre> </div>Renato OliveiraWed, 10 Aug 2016 15:26:04 -0000https://sourceforge.net8fa7610f8cf88d7decf6e8472313d1bc329c311b