{"title":"sleuth","link":[{"@attributes":{"href":"http:\/\/pachterlab.github.io\/sleuth\/","rel":"self"}},{"@attributes":{"href":"http:\/\/pachterlab.github.io\/sleuth"}}],"updated":"2019-06-19T05:46:02+00:00","id":"http:\/\/pachterlab.github.io\/sleuth","author":{"name":"Pachter Lab","email":"blah@email.test"},"entry":[{"title":"V0.42.2.1","link":{"@attributes":{"href":"http:\/\/pachterlab.github.io\/sleuth\/releases\/2015\/07\/06\/v0.42.2.1"}},"updated":"2015-07-06T00:00:00+00:00","id":"http:\/\/pachterlab.github.io\/sleuth\/releases\/2015\/07\/06\/v0.42.2.1","content":"<p>A few bugfixes to v0.42.2 are included here:<\/p>\n\n<ul>\n  <li>Off-by-one error fix in pseudobam output for reads mapping to reverse strand<\/li>\n  <li>Rare segfault fix happening on Ubuntu 12.02<\/li>\n  <li><code class=\"highlighter-rouge\">-nan<\/code> values would sometimes show up in abundances in edge case<\/li>\n<\/ul>\n\n<p>It is recommended that users upgrade to this release.<\/p>\n\n"},{"title":"V0.42.2","link":{"@attributes":{"href":"http:\/\/pachterlab.github.io\/sleuth\/releases\/2015\/06\/09\/v0.42.2"}},"updated":"2015-06-09T00:00:00+00:00","id":"http:\/\/pachterlab.github.io\/sleuth\/releases\/2015\/06\/09\/v0.42.2","content":"<p>This is version 0.42.2 of Kallisto.<\/p>\n\n<p>Updates include<\/p>\n\n<ul>\n  <li><code class=\"highlighter-rouge\">index<\/code>\n    <ul>\n      <li>the index has been updated to include more of the transcript information<\/li>\n      <li>indices should be slightly smaller than before<\/li>\n      <li>indices constructed with previous versions will not work with this version, rerun your index command<\/li>\n    <\/ul>\n  <\/li>\n  <li><code class=\"highlighter-rouge\">quant<\/code>\n    <ul>\n      <li>Bootstraps can be run in multithreaded mode, use option <code class=\"highlighter-rouge\">-t<\/code> to specify number of threads<\/li>\n      <li>If only one read of a paired end maps, <code class=\"highlighter-rouge\">kallisto<\/code> will check the transcript positions to discard reads that would go outside of transcript given the mean fragment length.<\/li>\n      <li>Pseudobam. Pseudoalignments can now be output in SAM format to standard output. For more details on the output see <a href=\"http:\/\/pachterlab.github.io\/kallisto\/pseudobam.html\">pseudobam<\/a><\/li>\n      <li>Sequence specific bias. <code class=\"highlighter-rouge\">kallisto<\/code> can learn a model for sequence specific bias and correct the abundances accordingly.<\/li>\n      <li>TSV. All output text files have been changed to <code class=\"highlighter-rouge\">.tsv<\/code> ending.<\/li>\n    <\/ul>\n  <\/li>\n<\/ul>\n\n"},{"title":"V0.42.1","link":{"@attributes":{"href":"http:\/\/pachterlab.github.io\/sleuth\/releases\/2015\/05\/12\/v0.42.1"}},"updated":"2015-05-12T00:00:00+00:00","id":"http:\/\/pachterlab.github.io\/sleuth\/releases\/2015\/05\/12\/v0.42.1","content":"<p>This is version 0.42.1 of Kallisto. We recommend that users upgrade to this version.<\/p>\n\n<p>Updates include<\/p>\n\n<ul>\n  <li><code class=\"highlighter-rouge\">index<\/code>\n    <ul>\n      <li>now accepts multiple FASTA files and creates an index of all the targets<\/li>\n      <li>clips the polyA tail of transcripts that end with runs of A of length 10 or greater<\/li>\n    <\/ul>\n  <\/li>\n  <li><code class=\"highlighter-rouge\">quant<\/code>\n    <ul>\n      <li>now accepts multiple FASTQ paired-end files, or single-end files<\/li>\n      <li><code class=\"highlighter-rouge\">--single<\/code> flag to specify single-end reads<\/li>\n      <li>simplifies jumping rules<\/li>\n      <li>uses soft-intersect, if one read has no mapping k-mers the other end is used for pseudoalignment<\/li>\n      <li>outputs number of reads processed and number of reads pseudoaligned<\/li>\n    <\/ul>\n  <\/li>\n<\/ul>\n\n"},{"title":"V0.42","link":{"@attributes":{"href":"http:\/\/pachterlab.github.io\/sleuth\/releases\/2015\/05\/06\/v0.42"}},"updated":"2015-05-06T00:00:00+00:00","id":"http:\/\/pachterlab.github.io\/sleuth\/releases\/2015\/05\/06\/v0.42","content":"<p>This is the initial public release of Kallisto.<\/p>\n\n"}]}