Loading MANUAL +25 −13 Original line number Diff line number Diff line Loading @@ -705,6 +705,18 @@ The query input files (specified either as `<m1>` and `<m2>`, or as or similar). All quality values are assumed to be 40 on the [Phred quality] scale. -F Reads are substrings (k-mers) extracted from a FASTA file `s`. Specifically, for every reference sequence in FASTA file `s`, Bowtie 2 aligns the k-mers at offsets 1, 1+i, 1+2i, ... until reaching the end of the reference. Each k-mer is aligned as a separate read. Quality values are set to all Is (40 on Phred scale). Each k-mer (read) is given a name like `sequence`_`offset`, where `sequence` is the name of the FASTA sequence it was drawn from and `offset` is its 0-based offset of origin with respect to the sequence. Only single k-mers, i.e. unpaired reads, can be aligned in this way. -r The query input files (specified either as `<m1>` and `<m2>`, or as Loading MANUAL.markdown +31 −14 Original line number Diff line number Diff line Loading @@ -767,6 +767,24 @@ The query input files (specified either as `<m1>` and `<m2>`, or as or similar). All quality values are assumed to be 40 on the [Phred quality] scale. </td></tr><tr><td id="bowtie-options-F"> [`-F`]: #bowtie-options-F -F </td><td> Reads are substrings (k-mers) extracted from a FASTA file `s`. Specifically, for every reference sequence in FASTA file `s`, Bowtie 2 aligns the k-mers at offsets 1, 1+i, 1+2i, ... until reaching the end of the reference. Each k-mer is aligned as a separate read. Quality values are set to all Is (40 on Phred scale). Each k-mer (read) is given a name like `sequence`_`offset`, where `sequence` is the name of the FASTA sequence it was drawn from and `offset` is its 0-based offset of origin with respect to the sequence. Only single k-mers, i.e. unpaired reads, can be aligned in this way. </td></tr><tr><td id="bowtie-options-r"> [`-r`]: #bowtie-options-r Loading Loading @@ -2425,4 +2443,3 @@ Print version information and quit. Print usage information and quit. </td></tr></table> Makefile +2 −1 Original line number Diff line number Diff line Loading @@ -420,9 +420,10 @@ doc: doc/manual.html MANUAL doc/manual.html: MANUAL.markdown echo "<h1>Table of Contents</h1>" > .tmp.head pandoc -T "Bowtie Manual" -B .tmp.head \ pandoc -B .tmp.head \ --css style.css -o $@ \ --from markdown --to HTML \ --metadata title:"Bowtie Manual" \ --table-of-contents $^ MANUAL: MANUAL.markdown Loading NEWS +16 −2 Original line number Diff line number Diff line Loading @@ -5,14 +5,15 @@ Bowtie NEWS Bowtie is now available for download. 0.9.0 is the first version to be released under the OSI Artistic License (see `LICENSE') and freely available to the public for download. The current version is 1.2.1.1. available to the public for download. The current version is 1.2.3. Reporting Issues ================ Please report any issues using the Sourceforge bug tracker: https://sourceforge.net/tracker/?group_id=236897&atid=1101606 * https://github.com/BenLangmead/bowtie/issues * https://sourceforge.net/tracker/?group_id=236897&atid=1101606 Announcements ============= Loading @@ -26,7 +27,20 @@ subscribe to our mailing list: Version Release History ======================= Version 1.2.3 - Jul 5, 2019 * Added support for reading and inspecting Bowtie 2 indexes. Bowtie 2 indexes can now be used with either Bowtie or Bowtie 2. * Added support for building an index from a gzipped-compressed FASTA. * Fixed issue preventing bowtie from reporting repeated alignments when -M is specified. * Fixed issue with -F mode omitting final base of each read. * Fixed clipping of first letter of first read in batches after first. * Fixed an issue preventing bowtie wrapper script from finding indexes. Version 1.2.2 - Dec 11, 2017 Update (12/12/2017): We have had to re-release this version of bowtie to address an issue when compiling with pthreads (make NO_TBB=1). * Fixed major issue causing corrupt SAM output when using many threads (-p/--threads) on certain systems * Fixed major issue with incorrect alignment offsets being reported in --large-index mode * Fixed major issue with reads files being skipped when multiple inputs were specified together with -p/--threads Loading VERSION +1 −1 Original line number Diff line number Diff line 1.2.2 1.2.3 Loading
MANUAL +25 −13 Original line number Diff line number Diff line Loading @@ -705,6 +705,18 @@ The query input files (specified either as `<m1>` and `<m2>`, or as or similar). All quality values are assumed to be 40 on the [Phred quality] scale. -F Reads are substrings (k-mers) extracted from a FASTA file `s`. Specifically, for every reference sequence in FASTA file `s`, Bowtie 2 aligns the k-mers at offsets 1, 1+i, 1+2i, ... until reaching the end of the reference. Each k-mer is aligned as a separate read. Quality values are set to all Is (40 on Phred scale). Each k-mer (read) is given a name like `sequence`_`offset`, where `sequence` is the name of the FASTA sequence it was drawn from and `offset` is its 0-based offset of origin with respect to the sequence. Only single k-mers, i.e. unpaired reads, can be aligned in this way. -r The query input files (specified either as `<m1>` and `<m2>`, or as Loading
MANUAL.markdown +31 −14 Original line number Diff line number Diff line Loading @@ -767,6 +767,24 @@ The query input files (specified either as `<m1>` and `<m2>`, or as or similar). All quality values are assumed to be 40 on the [Phred quality] scale. </td></tr><tr><td id="bowtie-options-F"> [`-F`]: #bowtie-options-F -F </td><td> Reads are substrings (k-mers) extracted from a FASTA file `s`. Specifically, for every reference sequence in FASTA file `s`, Bowtie 2 aligns the k-mers at offsets 1, 1+i, 1+2i, ... until reaching the end of the reference. Each k-mer is aligned as a separate read. Quality values are set to all Is (40 on Phred scale). Each k-mer (read) is given a name like `sequence`_`offset`, where `sequence` is the name of the FASTA sequence it was drawn from and `offset` is its 0-based offset of origin with respect to the sequence. Only single k-mers, i.e. unpaired reads, can be aligned in this way. </td></tr><tr><td id="bowtie-options-r"> [`-r`]: #bowtie-options-r Loading Loading @@ -2425,4 +2443,3 @@ Print version information and quit. Print usage information and quit. </td></tr></table>
Makefile +2 −1 Original line number Diff line number Diff line Loading @@ -420,9 +420,10 @@ doc: doc/manual.html MANUAL doc/manual.html: MANUAL.markdown echo "<h1>Table of Contents</h1>" > .tmp.head pandoc -T "Bowtie Manual" -B .tmp.head \ pandoc -B .tmp.head \ --css style.css -o $@ \ --from markdown --to HTML \ --metadata title:"Bowtie Manual" \ --table-of-contents $^ MANUAL: MANUAL.markdown Loading
NEWS +16 −2 Original line number Diff line number Diff line Loading @@ -5,14 +5,15 @@ Bowtie NEWS Bowtie is now available for download. 0.9.0 is the first version to be released under the OSI Artistic License (see `LICENSE') and freely available to the public for download. The current version is 1.2.1.1. available to the public for download. The current version is 1.2.3. Reporting Issues ================ Please report any issues using the Sourceforge bug tracker: https://sourceforge.net/tracker/?group_id=236897&atid=1101606 * https://github.com/BenLangmead/bowtie/issues * https://sourceforge.net/tracker/?group_id=236897&atid=1101606 Announcements ============= Loading @@ -26,7 +27,20 @@ subscribe to our mailing list: Version Release History ======================= Version 1.2.3 - Jul 5, 2019 * Added support for reading and inspecting Bowtie 2 indexes. Bowtie 2 indexes can now be used with either Bowtie or Bowtie 2. * Added support for building an index from a gzipped-compressed FASTA. * Fixed issue preventing bowtie from reporting repeated alignments when -M is specified. * Fixed issue with -F mode omitting final base of each read. * Fixed clipping of first letter of first read in batches after first. * Fixed an issue preventing bowtie wrapper script from finding indexes. Version 1.2.2 - Dec 11, 2017 Update (12/12/2017): We have had to re-release this version of bowtie to address an issue when compiling with pthreads (make NO_TBB=1). * Fixed major issue causing corrupt SAM output when using many threads (-p/--threads) on certain systems * Fixed major issue with incorrect alignment offsets being reported in --large-index mode * Fixed major issue with reads files being skipped when multiple inputs were specified together with -p/--threads Loading
