Loading CHANGES.rst +16 −0 Original line number Diff line number Diff line Loading @@ -2,6 +2,22 @@ Changes ======= v2.5 (2019-09-04) ----------------- * :issue:`391`: Multicore is now supported even when using ``--untrimmed-output``, ``--too-short-output``, ``--too-long-output`` or the corresponding ``...-paired-output`` options. * :issue:`393`: Using ``--info-file`` no longer crashes when processing paired-end data. However, the info file itself will only contain results for R1. * :issue:`394`: Options ``-e``/``--no-indels``/``-O`` were ignored for linked adapters * :issue:`320`: When a “Too many open files” error occurs during demultiplexing, Cutadapt can now automatically raise the limit and re-try if the limit is a “soft” limit. v2.4 (2019-07-09) ----------------- Loading PKG-INFO +7 −1 Original line number Diff line number Diff line Metadata-Version: 2.1 Name: cutadapt Version: 2.4 Version: 2.5 Summary: trim adapters from high-throughput sequencing reads Home-page: https://cutadapt.readthedocs.io/ Author: Marcel Martin Loading @@ -8,9 +8,15 @@ Author-email: marcel.martin@scilifelab.se License: MIT Description: .. image:: https://travis-ci.org/marcelm/cutadapt.svg?branch=master :target: https://travis-ci.org/marcelm/cutadapt :alt: .. image:: https://img.shields.io/pypi/v/cutadapt.svg?branch=master :target: https://pypi.python.org/pypi/cutadapt :alt: .. image:: https://codecov.io/gh/marcelm/cutadapt/branch/master/graph/badge.svg :target: https://codecov.io/gh/marcelm/cutadapt :alt: ======== Cutadapt Loading README.rst +6 −0 Original line number Diff line number Diff line .. image:: https://travis-ci.org/marcelm/cutadapt.svg?branch=master :target: https://travis-ci.org/marcelm/cutadapt :alt: .. image:: https://img.shields.io/pypi/v/cutadapt.svg?branch=master :target: https://pypi.python.org/pypi/cutadapt :alt: .. image:: https://codecov.io/gh/marcelm/cutadapt/branch/master/graph/badge.svg :target: https://codecov.io/gh/marcelm/cutadapt :alt: ======== Cutadapt Loading doc/algorithms.rst +1 −1 Original line number Diff line number Diff line Loading @@ -73,7 +73,7 @@ overlaps that are actually allowed by the adapter type are actually considered. .. _quality-trimming-algorithm: Quality trimming algorithm -------------------------- ========================== The trimming algorithm implemented in Cutadapt is the same as the one used by BWA, but applied to both Loading doc/guide.rst +24 −17 Original line number Diff line number Diff line Loading @@ -149,9 +149,6 @@ There are some limitations at the moment: - ``--info-file`` - ``--rest-file`` - ``--wildcard-file`` - ``--untrimmed-output``, ``--untrimmed-paired-output`` - ``--too-short-output``, ``--too-short-paired-output`` - ``--too-long-output``, ``--too-long-paired-output`` * Multi-core is also not compatible with ``--format`` Loading @@ -167,6 +164,10 @@ Some of these limitations will be lifted in the future, as time allows. .. versionadded:: 1.18 ``--cores=0`` for autodetection .. versionadded:: 2.5 Multicore works with ``--untrimmed/too-short/too-long-(paired)-output`` Speed-up tricks --------------- Loading Loading @@ -927,23 +928,29 @@ Quality trimming ---------------- The ``-q`` (or ``--quality-cutoff``) parameter can be used to trim low-quality ends from reads before adapter removal. For this to work correctly, the quality values must be encoded as ascii(phred quality + 33). If they are encoded as ascii(phred quality + 64), you need to add ``--quality-base=64`` to the command line. Quality trimming can be done without adapter trimming, so this will work:: low-quality ends from reads. If you specify a single cutoff value, the 3' end of each read is trimmed:: cutadapt -q 10 -o output.fastq input.fastq By default, only the 3' end of each read is quality-trimmed. If you want to trim the 5' end as well, use the ``-q`` option with two comma-separated cutoffs:: For Illumina reads, this is sufficient as their quality is high at the beginning, but degrades towards the 3' end. It is also possible to also trim from the 5' end by specifying two comma-separated cutoffs as *5' cutoff,3' cutoff*. For example, :: cutadapt -q 15,10 -o output.fastq input.fastq The 5' end will then be trimmed with a cutoff of 15, and the 3' end will be trimmed with a cutoff of 10. If you only want to trim the 5' end, then use a cutoff of 0 for the 3' end, as in ``-q 10,0``. will quality-trim the 5' end with a cutoff of 15 and the 3' end with a cutoff of 10. To only trim the 5' end, use a cutoff of 0 for the 3' end, as in ``-q 15,0``. Quality trimming is done before any adapter trimming. By default, quality values are assumed to be encoded as ascii(phred quality + 33). Nowadays, this should always be the case. Some old Illumina FASTQ files encode qualities as ascii(phred quality + 64). For those, you must add ``--quality-base=64`` to the command line. A :ref:`description of the quality-trimming algorithm is also available <quality-trimming-algorithm>`. The algorithm is the same as used by BWA. Loading @@ -955,11 +962,11 @@ Quality trimming of reads using two-color chemistry (NextSeq) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Some Illumina instruments use a two-color chemistry to encode the four bases. This includes the NextSeq and the (at the time of this writing) recently announced NovaSeq. In those instruments, a 'dark cycle' (with no detected color) This includes the NextSeq and the NovaSeq. In those instruments, a 'dark cycle' (with no detected color) encodes a ``G``. However, dark cycles also occur when when sequencing "falls off" the end of the fragment. The read then `contains a run of high-quality, but incorrect ``G`` calls <https://sequencing.qcfail.com/articles/illumina-2-colour-chemistry-can-overcall-high-confidence-g-bases/>`_ incorrect “G” calls <https://sequencing.qcfail.com/articles/illumina-2-colour-chemistry-can-overcall-high-confidence-g-bases/>`_ at its 3' end. Since the regular quality-trimming algorithm cannot deal with this situation, Loading Loading
CHANGES.rst +16 −0 Original line number Diff line number Diff line Loading @@ -2,6 +2,22 @@ Changes ======= v2.5 (2019-09-04) ----------------- * :issue:`391`: Multicore is now supported even when using ``--untrimmed-output``, ``--too-short-output``, ``--too-long-output`` or the corresponding ``...-paired-output`` options. * :issue:`393`: Using ``--info-file`` no longer crashes when processing paired-end data. However, the info file itself will only contain results for R1. * :issue:`394`: Options ``-e``/``--no-indels``/``-O`` were ignored for linked adapters * :issue:`320`: When a “Too many open files” error occurs during demultiplexing, Cutadapt can now automatically raise the limit and re-try if the limit is a “soft” limit. v2.4 (2019-07-09) ----------------- Loading
PKG-INFO +7 −1 Original line number Diff line number Diff line Metadata-Version: 2.1 Name: cutadapt Version: 2.4 Version: 2.5 Summary: trim adapters from high-throughput sequencing reads Home-page: https://cutadapt.readthedocs.io/ Author: Marcel Martin Loading @@ -8,9 +8,15 @@ Author-email: marcel.martin@scilifelab.se License: MIT Description: .. image:: https://travis-ci.org/marcelm/cutadapt.svg?branch=master :target: https://travis-ci.org/marcelm/cutadapt :alt: .. image:: https://img.shields.io/pypi/v/cutadapt.svg?branch=master :target: https://pypi.python.org/pypi/cutadapt :alt: .. image:: https://codecov.io/gh/marcelm/cutadapt/branch/master/graph/badge.svg :target: https://codecov.io/gh/marcelm/cutadapt :alt: ======== Cutadapt Loading
README.rst +6 −0 Original line number Diff line number Diff line .. image:: https://travis-ci.org/marcelm/cutadapt.svg?branch=master :target: https://travis-ci.org/marcelm/cutadapt :alt: .. image:: https://img.shields.io/pypi/v/cutadapt.svg?branch=master :target: https://pypi.python.org/pypi/cutadapt :alt: .. image:: https://codecov.io/gh/marcelm/cutadapt/branch/master/graph/badge.svg :target: https://codecov.io/gh/marcelm/cutadapt :alt: ======== Cutadapt Loading
doc/algorithms.rst +1 −1 Original line number Diff line number Diff line Loading @@ -73,7 +73,7 @@ overlaps that are actually allowed by the adapter type are actually considered. .. _quality-trimming-algorithm: Quality trimming algorithm -------------------------- ========================== The trimming algorithm implemented in Cutadapt is the same as the one used by BWA, but applied to both Loading
doc/guide.rst +24 −17 Original line number Diff line number Diff line Loading @@ -149,9 +149,6 @@ There are some limitations at the moment: - ``--info-file`` - ``--rest-file`` - ``--wildcard-file`` - ``--untrimmed-output``, ``--untrimmed-paired-output`` - ``--too-short-output``, ``--too-short-paired-output`` - ``--too-long-output``, ``--too-long-paired-output`` * Multi-core is also not compatible with ``--format`` Loading @@ -167,6 +164,10 @@ Some of these limitations will be lifted in the future, as time allows. .. versionadded:: 1.18 ``--cores=0`` for autodetection .. versionadded:: 2.5 Multicore works with ``--untrimmed/too-short/too-long-(paired)-output`` Speed-up tricks --------------- Loading Loading @@ -927,23 +928,29 @@ Quality trimming ---------------- The ``-q`` (or ``--quality-cutoff``) parameter can be used to trim low-quality ends from reads before adapter removal. For this to work correctly, the quality values must be encoded as ascii(phred quality + 33). If they are encoded as ascii(phred quality + 64), you need to add ``--quality-base=64`` to the command line. Quality trimming can be done without adapter trimming, so this will work:: low-quality ends from reads. If you specify a single cutoff value, the 3' end of each read is trimmed:: cutadapt -q 10 -o output.fastq input.fastq By default, only the 3' end of each read is quality-trimmed. If you want to trim the 5' end as well, use the ``-q`` option with two comma-separated cutoffs:: For Illumina reads, this is sufficient as their quality is high at the beginning, but degrades towards the 3' end. It is also possible to also trim from the 5' end by specifying two comma-separated cutoffs as *5' cutoff,3' cutoff*. For example, :: cutadapt -q 15,10 -o output.fastq input.fastq The 5' end will then be trimmed with a cutoff of 15, and the 3' end will be trimmed with a cutoff of 10. If you only want to trim the 5' end, then use a cutoff of 0 for the 3' end, as in ``-q 10,0``. will quality-trim the 5' end with a cutoff of 15 and the 3' end with a cutoff of 10. To only trim the 5' end, use a cutoff of 0 for the 3' end, as in ``-q 15,0``. Quality trimming is done before any adapter trimming. By default, quality values are assumed to be encoded as ascii(phred quality + 33). Nowadays, this should always be the case. Some old Illumina FASTQ files encode qualities as ascii(phred quality + 64). For those, you must add ``--quality-base=64`` to the command line. A :ref:`description of the quality-trimming algorithm is also available <quality-trimming-algorithm>`. The algorithm is the same as used by BWA. Loading @@ -955,11 +962,11 @@ Quality trimming of reads using two-color chemistry (NextSeq) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Some Illumina instruments use a two-color chemistry to encode the four bases. This includes the NextSeq and the (at the time of this writing) recently announced NovaSeq. In those instruments, a 'dark cycle' (with no detected color) This includes the NextSeq and the NovaSeq. In those instruments, a 'dark cycle' (with no detected color) encodes a ``G``. However, dark cycles also occur when when sequencing "falls off" the end of the fragment. The read then `contains a run of high-quality, but incorrect ``G`` calls <https://sequencing.qcfail.com/articles/illumina-2-colour-chemistry-can-overcall-high-confidence-g-bases/>`_ incorrect “G” calls <https://sequencing.qcfail.com/articles/illumina-2-colour-chemistry-can-overcall-high-confidence-g-bases/>`_ at its 3' end. Since the regular quality-trimming algorithm cannot deal with this situation, Loading
